diff shm_downloads.htm @ 83:729738462297 draft

"planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
author rhpvorderman
date Wed, 15 Sep 2021 12:24:06 +0000
parents ba33b94637ca
children 6809c63d9161
line wrap: on
line diff
--- a/shm_downloads.htm	Thu Feb 25 10:32:32 2021 +0000
+++ b/shm_downloads.htm	Wed Sep 15 12:24:06 2021 +0000
@@ -1,538 +1,538 @@
-<html>
-
-<head>
-<meta http-equiv=Content-Type content="text/html; charset=windows-1252">
-<meta name=Generator content="Microsoft Word 14 (filtered)">
-<style>
-<!--
- /* Font Definitions */
- @font-face
-	{font-family:Calibri;
-	panose-1:2 15 5 2 2 2 4 3 2 4;}
- /* Style Definitions */
- p.MsoNormal, li.MsoNormal, div.MsoNormal
-	{margin-top:0in;
-	margin-right:0in;
-	margin-bottom:10.0pt;
-	margin-left:0in;
-	line-height:115%;
-	font-size:11.0pt;
-	font-family:"Calibri","sans-serif";}
-a:link, span.MsoHyperlink
-	{color:blue;
-	text-decoration:underline;}
-a:visited, span.MsoHyperlinkFollowed
-	{color:purple;
-	text-decoration:underline;}
-p.MsoNoSpacing, li.MsoNoSpacing, div.MsoNoSpacing
-	{margin:0in;
-	margin-bottom:.0001pt;
-	font-size:11.0pt;
-	font-family:"Calibri","sans-serif";}
-.MsoChpDefault
-	{font-family:"Calibri","sans-serif";}
-.MsoPapDefault
-	{margin-bottom:10.0pt;
-	line-height:115%;}
-@page WordSection1
-	{size:8.5in 11.0in;
-	margin:1.0in 1.0in 1.0in 1.0in;}
-div.WordSection1
-	{page:WordSection1;}
--->
-</style>
-
-</head>
-
-<body lang=EN-US link=blue vlink=purple>
-
-<div class=WordSection1>
-
-<p class=MsoNoSpacing style='text-align:justify'><b><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Info</span></b></p>
-
-<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The complete
-dataset:</span></u><span lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'>
-Allows downloading of the complete parsed data set.</span></p>
-
-<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The filtered
-dataset:</span></u><span lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'>
-Allows downloading of all parsed IMGT information of all transcripts that
-passed the chosen filter settings.</span></p>
-
-<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The alignment
-info on the unmatched sequences:</span></u><span lang=EN-GB style='font-size:
-12.0pt;font-family:"Times New Roman","serif"'> Provides information of the subclass
-alignment of all unmatched sequences. For each sequence the chunck hit
-percentage and the nt hit percentage is shown together with the best matched
-subclass.</span></p>
-
-<p class=MsoNoSpacing style='text-align:justify'><b><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>SHM Overview</span></b></p>
-
-<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The SHM Overview
-table as a dataset:</span></u><span lang=EN-GB style='font-size:12.0pt;
-font-family:"Times New Roman","serif"'> Allows downloading of the SHM Overview
-table as a data set.  </span></p>
-
-<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Motif data per
-sequence ID:</span></u><span lang=EN-GB style='font-size:12.0pt;font-family:
-"Times New Roman","serif"'> Provides a file that contains information for each
-transcript on the number of mutations present in WA/TW and RGYW/WRCY motives.</span></p>
-
-<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Mutation data
-per sequence ID: </span></u><span lang=EN-GB style='font-size:12.0pt;
-font-family:"Times New Roman","serif"'>Provides a file containing information
-on the number of sequences bases, the number and location of mutations and the
-type of mutations found in each transcript. </span></p>
-
-<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Base count for
-every sequence:</span></u><span lang=EN-GB style='font-size:12.0pt;font-family:
-"Times New Roman","serif"'> links to a page showing for each transcript the
-sequence of the analysed region (as dependent on the sequence starts at filter),
-the assigned subclass and the number of sequenced A,C,G and T’s.</span></p>
-
-<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The data used to
-generate the percentage of mutations in AID and pol eta motives plot:</span></u><span
-lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'>
-Provides a file containing the values used to generate the percentage of
-mutations in AID and pol eta motives plot in the SHM overview tab.</span></p>
-
-<p class=MsoNormalCxSpFirst style='text-align:justify'><u><span lang=EN-GB
-style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
-data used to generate the relative mutation patterns plot:</span></u><span
-lang=EN-GB style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
-Provides a download with the data used to generate the relative mutation
-patterns plot in the SHM overview tab.</span></p>
-
-<p class=MsoNormalCxSpLast style='text-align:justify'><u><span lang=EN-GB
-style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
-data used to generate the absolute mutation patterns plot:</span></u><span
-lang=EN-GB style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
-Provides a download with the data used to generate the absolute mutation
-patterns plot in the SHM overview tab. </span></p>
-
-<p class=MsoNoSpacing style='text-align:justify'><b><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>SHM Frequency</span></b></p>
-
-<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The data
-generate the frequency scatter plot:</span></u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'> Allows
-downloading the data used to generate the frequency scatter plot in the SHM
-frequency tab. </span></p>
-
-<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The data used to
-generate the frequency by class plot:</span></u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'> Allows
-downloading the data used to generate frequency by class plot included in the
-SHM frequency tab.           </span></p>
-
-<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The data for
-frequency by subclass:</span></u><span lang=EN-GB style='font-size:12.0pt;
-font-family:"Times New Roman","serif"'> Provides information of the number and
-percentage of sequences that have 0%, 0-2%, 2-5%, 5-10%, 10-15%, 15-20%,
-&gt;20% SHM. Information is provided for each subclass.</span></p>
-
-<p class=MsoNoSpacing style='text-align:justify'><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'> </span></p>
-
-<p class=MsoNoSpacing style='text-align:justify'><b><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Transition
-Tables</span></b></p>
-
-<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The data for the
-'all' transition plot:</span></u><span lang=EN-GB style='font-size:12.0pt;
-font-family:"Times New Roman","serif"'> Contains the information used to
-generate the transition table for all sequences.</span></p>
-
-<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The data for the
-'IGA' transition plot:</span></u><span lang=EN-GB style='font-size:12.0pt;
-font-family:"Times New Roman","serif"'> Contains the information used to
-generate the transition table for all IGA sequences.</span></p>
-
-<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The data for the
-'IGA1' transition plot:</span></u><span lang=EN-GB style='font-size:12.0pt;
-font-family:"Times New Roman","serif"'> Contains the information used to
-generate the transition table for all IGA1 sequences.</span></p>
-
-<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The data for the
-'IGA2' transition plot:</span></u><span lang=EN-GB style='font-size:12.0pt;
-font-family:"Times New Roman","serif"'> Contains the information used to
-generate the transition table for all IGA2 sequences.</span></p>
-
-<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The data for the
-'IGG' transition plot :</span></u><span lang=EN-GB style='font-size:12.0pt;
-font-family:"Times New Roman","serif"'> Contains the information used to
-generate the transition table for all IGG sequences.</span></p>
-
-<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The data for the
-'IGG1' transition plot:</span></u><span lang=EN-GB style='font-size:12.0pt;
-font-family:"Times New Roman","serif"'> Contains the information used to
-generate the transition table for all IGG1 sequences.</span></p>
-
-<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The data for the
-'IGG2' transition plot:</span></u><span lang=EN-GB style='font-size:12.0pt;
-font-family:"Times New Roman","serif"'> Contains the information used to
-generate the transition table for all IGG2 sequences.</span></p>
-
-<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The data for the
-'IGG3' transition plot:</span></u><span lang=EN-GB style='font-size:12.0pt;
-font-family:"Times New Roman","serif"'> Contains the information used to
-generate the transition table for all IGG3 sequences.</span></p>
-
-<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The data for the
-'IGG4' transition plot:</span></u><span lang=EN-GB style='font-size:12.0pt;
-font-family:"Times New Roman","serif"'> Contains the information used to
-generate the transition table for all IGG4 sequences.</span></p>
-
-<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The data for the
-'IGM' transition plot :</span></u><span lang=EN-GB style='font-size:12.0pt;
-font-family:"Times New Roman","serif"'> Contains the information used to
-generate the transition table for all IGM sequences.</span></p>
-
-<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The data for the
-'IGE' transition plot:</span></u><span lang=EN-GB style='font-size:12.0pt;
-font-family:"Times New Roman","serif"'> Contains the
-information used to generate the transition table for all IGE sequences.</span></p>
-
-<p class=MsoNoSpacing style='text-align:justify'><b><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Antigen
-selection</span></b></p>
-
-<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>AA mutation data
-per sequence ID:</span></u><span lang=EN-GB style='font-size:12.0pt;font-family:
-"Times New Roman","serif"'> Provides for each transcript information on whether
-there is replacement mutation at each amino acid location (as defined by IMGT).
-For all amino acids outside of the analysed region the value 0 is given.</span></p>
-
-<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Presence of AA
-per sequence ID:</span></u><span lang=EN-GB style='font-size:12.0pt;font-family:
-"Times New Roman","serif"'> Provides for each transcript information on which
-amino acid location (as defined by IMGT) is present. </span><span lang=NL
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>0 is absent, 1
-is present. </span></p>
-
-<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The data used to
-generate the aa mutation frequency plot:</span></u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'> Provides the
-data used to generate the aa mutation frequency plot for all sequences in the
-antigen selection tab.</span></p>
-
-<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The data used to
-generate the aa mutation frequency plot for IGA:</span></u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>  Provides the
-data used to generate the aa mutation frequency plot for all IGA sequences in
-the antigen selection tab.</span></p>
-
-<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The data used to
-generate the aa mutation frequency plot for IGG:</span></u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'> Provides the
-data used to generate the aa mutation frequency plot for all IGG sequences in
-the antigen selection tab.</span></p>
-
-<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The data used to
-generate the aa mutation frequency plot for IGM:</span></u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'> Provides the
-data used to generate the aa mutation frequency plot for all IGM sequences in
-the antigen selection tab.</span></p>
-
-<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The data used to
-generate the aa mutation frequency plot for IGE:</span></u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>   Provides the
-data used to generate the aa mutation frequency plot for all IGE sequences in
-the antigen selection tab.</span></p>
-
-<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Baseline PDF (</span></u><span
-lang=EN-GB><a href="http://selection.med.yale.edu/baseline/"><span
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>http://selection.med.yale.edu/baseline/</span></a></span><u><span
-lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'>):</span></u><span
-lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'> PDF
-containing the </span><span lang=EN-GB style='font-size:12.0pt;font-family:
-"Times New Roman","serif"'>Antigen selection (BASELINe) graph for all
-sequences.</span></p>
-
-<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Baseline data:</span></u><span
-lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'>
-Table output of the BASELINe analysis. Calculation of antigen selection as
-performed by BASELINe are shown for each individual sequence and the sum of all
-sequences.</span></p>
-
-<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Baseline IGA
-PDF:</span></u><span lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'>
-PDF containing the </span><span lang=EN-GB style='font-size:12.0pt;font-family:
-"Times New Roman","serif"'>Antigen selection (BASELINe) graph for all
-sequences.</span></p>
-
-<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Baseline IGA
-data:</span></u><span lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'>
-Table output of the BASELINe analysis. Calculation of antigen selection as
-performed by BASELINe are shown for each individual IGA sequence and the sum of
-all IGA sequences.</span></p>
-
-<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Baseline IGG
-PDF:</span></u><span lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'>
-PDF containing the </span><span lang=EN-GB style='font-size:12.0pt;font-family:
-"Times New Roman","serif"'>Antigen selection (BASELINe) graph for all IGG
-sequences.</span></p>
-
-<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Baseline IGG
-data:</span></u><span lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'>
-Table output of the BASELINe analysis. Calculation of antigen selection as
-performed by BASELINe are shown for each individual IGG sequence and the sum of
-all IGG sequences.        </span></p>
-
-<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Baseline IGM PDF:</span></u><span
-lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'> PDF
-containing the </span><span lang=EN-GB style='font-size:12.0pt;font-family:
-"Times New Roman","serif"'>Antigen selection (BASELINe) graph for all IGM
-sequences.</span></p>
-
-<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Baseline IGM
-data:</span></u><span lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'>
-Table output of the BASELINe analysis. Calculation of antigen selection as
-performed by BASELINe are shown for each individual IGM sequence and the sum of
-all IGM sequences.</span></p>
-
-<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Baseline IGE
-PDF:</span></u><span lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'>
-PDF containing the </span><span lang=EN-GB style='font-size:12.0pt;font-family:
-"Times New Roman","serif"'>Antigen selection (BASELINe) graph for all IGE
-sequences.</span><span lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'>
-</span></p>
-
-<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Baseline IGE
-data:</span></u><span lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'>
-Table output of the BASELINe analysis. Calculation of antigen selection as
-performed by BASELINe are shown for each individual IGE sequence and the sum of
-all IGE sequences.</span></p>
-
-<p class=MsoNoSpacing style='text-align:justify'><b><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>CSR</span></b></p>
-
-<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The data for the
-</span></u><u><span lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'>IGA
-subclass distribution plot :</span></u><span lang=EN-GB style='font-size:12.0pt;
-font-family:"Times New Roman","serif"'> </span><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Data used for
-the generation of the </span><span lang=EN-GB style='font-size:12.0pt;
-font-family:"Times New Roman","serif"'>IGA subclass distribution plot provided
-in the CSR tab. </span></p>
-
-<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The data for the
-</span></u><u><span lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'>IGA
-subclass distribution plot :</span></u><span lang=EN-GB style='font-size:12.0pt;
-font-family:"Times New Roman","serif"'> Data used for the generation of the </span><span
-lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'>IGG
-subclass distribution plot provided in the CSR tab. </span></p>
-
-<p class=MsoNoSpacing style='text-align:justify'><b><span lang=NL
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Clonal relation</span></b></p>
-
-<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Sequence overlap
-between subclasses:</span></u><span lang=EN-GB style='font-size:12.0pt;
-font-family:"Times New Roman","serif"'> Link to the overlap table as provided
-under the clonality overlap tab.         </span></p>
-
-<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The Change-O DB
-file with defined clones and subclass annotation:</span></u><span
-lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'>
-Downloads a table with the calculation of clonal relation between all
-sequences. For each individual transcript the results of the clonal assignment
-as provided by Change-O are provided. Sequences with the same number in the CLONE
-column are considered clonally related. </span></p>
-
-<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The Change-O DB
-defined clones summary file:</span></u><span lang=EN-GB style='font-size:12.0pt;
-font-family:"Times New Roman","serif"'> Gives a summary of the total number of
-clones in all sequences and their clone size.           </span></p>
-
-<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The Change-O DB
-file with defined clones of IGA:</span></u><span lang=EN-GB style='font-size:
-12.0pt;font-family:"Times New Roman","serif"'> Downloads a table with the
-calculation of clonal relation between all IGA sequences. For each individual
-transcript the results of the clonal assignment as provided by Change-O are
-provided. Sequences with the same number in the CLONE column are considered
-clonally related. </span></p>
-
-<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The Change-O DB
-defined clones summary file of IGA:</span></u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'> Gives a summary
-of the total number of clones in all IGA sequences and their clone size.</span></p>
-
-<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The Change-O DB
-file with defined clones of IGG:</span></u><span lang=EN-GB style='font-size:
-12.0pt;font-family:"Times New Roman","serif"'> Downloads a table with the
-calculation of clonal relation between all IGG sequences. For each individual
-transcript the results of the clonal assignment as provided by Change-O are
-provided. Sequences with the same number in the CLONE column are considered
-clonally related. </span></p>
-
-<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The Change-O DB
-defined clones summary file of IGG:</span></u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'> Gives a summary
-of the total number of clones in all IGG sequences and their clone size.</span></p>
-
-<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The Change-O DB
-file with defined clones of IGM:</span></u><span lang=EN-GB style='font-size:
-12.0pt;font-family:"Times New Roman","serif"'> Downloads a table
-with the calculation of clonal relation between all IGM sequences. For each
-individual transcript the results of the clonal assignment as provided by
-Change-O are provided. Sequences with the same number in the CLONE column are
-considered clonally related. </span></p>
-
-<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The Change-O DB
-defined clones summary file of IGM:</span></u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'> Gives a summary
-of the total number of clones in all IGM sequences and their clone size.</span></p>
-
-<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The Change-O DB
-file with defined clones of IGE:</span></u><span lang=EN-GB style='font-size:
-12.0pt;font-family:"Times New Roman","serif"'> Downloads a table with the
-calculation of clonal relation between all IGE sequences. For each individual
-transcript the results of the clonal assignment as provided by Change-O are
-provided. Sequences with the same number in the CLONE column are considered
-clonally related. </span></p>
-
-<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The Change-O DB
-defined clones summary file of IGE:</span></u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'> Gives a summary
-of the total number of clones in all IGE sequences and their clone size.</span></p>
-
-<p class=MsoNoSpacing style='text-align:justify'><b><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Filtered IMGT
-output files</span></b></p>
-
-<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>An IMGT archive
-with just the matched and filtered sequences:</span></u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'> Downloads a
-.txz file with the same format as downloaded IMGT files that contains all
-sequences that have passed the chosen filter settings.</span></p>
-
-<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>An IMGT archive
-with just the matched and filtered IGA sequences:</span></u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'> Downloads a
-.txz file with the same format as downloaded IMGT files that contains all IGA
-sequences that have passed the chosen filter settings.</span></p>
-
-<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>An IMGT archive
-with just the matched and filtered IGA1 sequences:</span></u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'> Downloads a
-.txz file with the same format as downloaded IMGT files that contains all IGA1
-sequences that have passed the chosen filter settings.</span></p>
-
-<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>An IMGT archive
-with just the matched and filtered IGA2 sequences:</span></u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'> Downloads a .txz
-file with the same format as downloaded IMGT files that contains all IGA2
-sequences that have passed the chosen filter settings.</span></p>
-
-<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>An IMGT archive
-with just the matched and filtered IGG sequences:</span></u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'> Downloads a .txz
-file with the same format as downloaded IMGT files that contains all IGG
-sequences that have passed the chosen filter settings.</span></p>
-
-<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>An IMGT archive
-with just the matched and filtered IGG1 sequences:</span></u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'> Downloads a
-.txz file with the same format as downloaded IMGT files that contains all IGG1
-sequences that have passed the chosen filter settings.</span></p>
-
-<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>An IMGT archive
-with just the matched and filtered IGG2 sequences:</span></u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'> Downloads a
-.txz file with the same format as downloaded IMGT files that contains all IGG2
-sequences that have passed the chosen filter settings.</span></p>
-
-<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>An IMGT archive
-with just the matched and filtered IGG3 sequences:</span></u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'> Downloads a .txz
-file with the same format as downloaded IMGT files that contains all IGG3
-sequences that have passed the chosen filter settings.</span></p>
-
-<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>An IMGT archive
-with just the matched and filtered IGG4 sequences:</span></u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'> Downloads a
-.txz file with the same format as downloaded IMGT files that contains all IGG4
-sequences that have passed the chosen filter settings.</span></p>
-
-<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>An IMGT archive
-with just the matched and filtered IGM sequences:</span></u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'> Downloads a .txz
-file with the same format as downloaded IMGT files that contains all IGM
-sequences that have passed the chosen filter settings.</span></p>
-
-<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'>An IMGT archive
-with just the matched and filtered IGE sequences:</span></u><span lang=EN-GB
-style='font-size:12.0pt;font-family:"Times New Roman","serif"'> Downloads a
-.txz file with the same format as downloaded IMGT files that contains all IGE
-sequences that have passed the chosen filter settings.</span></p>
-
-</div>
-
-</body>
-
-</html>
+<html>
+
+<head>
+<meta http-equiv=Content-Type content="text/html; charset=windows-1252">
+<meta name=Generator content="Microsoft Word 14 (filtered)">
+<style>
+<!--
+ /* Font Definitions */
+ @font-face
+	{font-family:Calibri;
+	panose-1:2 15 5 2 2 2 4 3 2 4;}
+ /* Style Definitions */
+ p.MsoNormal, li.MsoNormal, div.MsoNormal
+	{margin-top:0in;
+	margin-right:0in;
+	margin-bottom:10.0pt;
+	margin-left:0in;
+	line-height:115%;
+	font-size:11.0pt;
+	font-family:"Calibri","sans-serif";}
+a:link, span.MsoHyperlink
+	{color:blue;
+	text-decoration:underline;}
+a:visited, span.MsoHyperlinkFollowed
+	{color:purple;
+	text-decoration:underline;}
+p.MsoNoSpacing, li.MsoNoSpacing, div.MsoNoSpacing
+	{margin:0in;
+	margin-bottom:.0001pt;
+	font-size:11.0pt;
+	font-family:"Calibri","sans-serif";}
+.MsoChpDefault
+	{font-family:"Calibri","sans-serif";}
+.MsoPapDefault
+	{margin-bottom:10.0pt;
+	line-height:115%;}
+@page WordSection1
+	{size:8.5in 11.0in;
+	margin:1.0in 1.0in 1.0in 1.0in;}
+div.WordSection1
+	{page:WordSection1;}
+-->
+</style>
+
+</head>
+
+<body lang=EN-US link=blue vlink=purple>
+
+<div class=WordSection1>
+
+<p class=MsoNoSpacing style='text-align:justify'><b><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Info</span></b></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The complete
+dataset:</span></u><span lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'>
+Allows downloading of the complete parsed data set.</span></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The filtered
+dataset:</span></u><span lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'>
+Allows downloading of all parsed IMGT information of all transcripts that
+passed the chosen filter settings.</span></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The alignment
+info on the unmatched sequences:</span></u><span lang=EN-GB style='font-size:
+12.0pt;font-family:"Times New Roman","serif"'> Provides information of the subclass
+alignment of all unmatched sequences. For each sequence the chunck hit
+percentage and the nt hit percentage is shown together with the best matched
+subclass.</span></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><b><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>SHM Overview</span></b></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The SHM Overview
+table as a dataset:</span></u><span lang=EN-GB style='font-size:12.0pt;
+font-family:"Times New Roman","serif"'> Allows downloading of the SHM Overview
+table as a data set.  </span></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Motif data per
+sequence ID:</span></u><span lang=EN-GB style='font-size:12.0pt;font-family:
+"Times New Roman","serif"'> Provides a file that contains information for each
+transcript on the number of mutations present in WA/TW and RGYW/WRCY motives.</span></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Mutation data
+per sequence ID: </span></u><span lang=EN-GB style='font-size:12.0pt;
+font-family:"Times New Roman","serif"'>Provides a file containing information
+on the number of sequences bases, the number and location of mutations and the
+type of mutations found in each transcript. </span></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Base count for
+every sequence:</span></u><span lang=EN-GB style='font-size:12.0pt;font-family:
+"Times New Roman","serif"'> links to a page showing for each transcript the
+sequence of the analysed region (as dependent on the sequence starts at filter),
+the assigned subclass and the number of sequenced A,C,G and T’s.</span></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The data used to
+generate the percentage of mutations in AID and pol eta motives plot:</span></u><span
+lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'>
+Provides a file containing the values used to generate the percentage of
+mutations in AID and pol eta motives plot in the SHM overview tab.</span></p>
+
+<p class=MsoNormalCxSpFirst style='text-align:justify'><u><span lang=EN-GB
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
+data used to generate the relative mutation patterns plot:</span></u><span
+lang=EN-GB style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
+Provides a download with the data used to generate the relative mutation
+patterns plot in the SHM overview tab.</span></p>
+
+<p class=MsoNormalCxSpLast style='text-align:justify'><u><span lang=EN-GB
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
+data used to generate the absolute mutation patterns plot:</span></u><span
+lang=EN-GB style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
+Provides a download with the data used to generate the absolute mutation
+patterns plot in the SHM overview tab. </span></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><b><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>SHM Frequency</span></b></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The data
+generate the frequency scatter plot:</span></u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'> Allows
+downloading the data used to generate the frequency scatter plot in the SHM
+frequency tab. </span></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The data used to
+generate the frequency by class plot:</span></u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'> Allows
+downloading the data used to generate frequency by class plot included in the
+SHM frequency tab.           </span></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The data for
+frequency by subclass:</span></u><span lang=EN-GB style='font-size:12.0pt;
+font-family:"Times New Roman","serif"'> Provides information of the number and
+percentage of sequences that have 0%, 0-2%, 2-5%, 5-10%, 10-15%, 15-20%,
+&gt;20% SHM. Information is provided for each subclass.</span></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'> </span></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><b><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Transition
+Tables</span></b></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The data for the
+'all' transition plot:</span></u><span lang=EN-GB style='font-size:12.0pt;
+font-family:"Times New Roman","serif"'> Contains the information used to
+generate the transition table for all sequences.</span></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The data for the
+'IGA' transition plot:</span></u><span lang=EN-GB style='font-size:12.0pt;
+font-family:"Times New Roman","serif"'> Contains the information used to
+generate the transition table for all IGA sequences.</span></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The data for the
+'IGA1' transition plot:</span></u><span lang=EN-GB style='font-size:12.0pt;
+font-family:"Times New Roman","serif"'> Contains the information used to
+generate the transition table for all IGA1 sequences.</span></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The data for the
+'IGA2' transition plot:</span></u><span lang=EN-GB style='font-size:12.0pt;
+font-family:"Times New Roman","serif"'> Contains the information used to
+generate the transition table for all IGA2 sequences.</span></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The data for the
+'IGG' transition plot :</span></u><span lang=EN-GB style='font-size:12.0pt;
+font-family:"Times New Roman","serif"'> Contains the information used to
+generate the transition table for all IGG sequences.</span></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The data for the
+'IGG1' transition plot:</span></u><span lang=EN-GB style='font-size:12.0pt;
+font-family:"Times New Roman","serif"'> Contains the information used to
+generate the transition table for all IGG1 sequences.</span></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The data for the
+'IGG2' transition plot:</span></u><span lang=EN-GB style='font-size:12.0pt;
+font-family:"Times New Roman","serif"'> Contains the information used to
+generate the transition table for all IGG2 sequences.</span></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The data for the
+'IGG3' transition plot:</span></u><span lang=EN-GB style='font-size:12.0pt;
+font-family:"Times New Roman","serif"'> Contains the information used to
+generate the transition table for all IGG3 sequences.</span></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The data for the
+'IGG4' transition plot:</span></u><span lang=EN-GB style='font-size:12.0pt;
+font-family:"Times New Roman","serif"'> Contains the information used to
+generate the transition table for all IGG4 sequences.</span></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The data for the
+'IGM' transition plot :</span></u><span lang=EN-GB style='font-size:12.0pt;
+font-family:"Times New Roman","serif"'> Contains the information used to
+generate the transition table for all IGM sequences.</span></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The data for the
+'IGE' transition plot:</span></u><span lang=EN-GB style='font-size:12.0pt;
+font-family:"Times New Roman","serif"'> Contains the
+information used to generate the transition table for all IGE sequences.</span></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><b><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Antigen
+selection</span></b></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>AA mutation data
+per sequence ID:</span></u><span lang=EN-GB style='font-size:12.0pt;font-family:
+"Times New Roman","serif"'> Provides for each transcript information on whether
+there is replacement mutation at each amino acid location (as defined by IMGT).
+For all amino acids outside of the analysed region the value 0 is given.</span></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Presence of AA
+per sequence ID:</span></u><span lang=EN-GB style='font-size:12.0pt;font-family:
+"Times New Roman","serif"'> Provides for each transcript information on which
+amino acid location (as defined by IMGT) is present. </span><span lang=NL
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>0 is absent, 1
+is present. </span></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The data used to
+generate the aa mutation frequency plot:</span></u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'> Provides the
+data used to generate the aa mutation frequency plot for all sequences in the
+antigen selection tab.</span></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The data used to
+generate the aa mutation frequency plot for IGA:</span></u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>  Provides the
+data used to generate the aa mutation frequency plot for all IGA sequences in
+the antigen selection tab.</span></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The data used to
+generate the aa mutation frequency plot for IGG:</span></u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'> Provides the
+data used to generate the aa mutation frequency plot for all IGG sequences in
+the antigen selection tab.</span></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The data used to
+generate the aa mutation frequency plot for IGM:</span></u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'> Provides the
+data used to generate the aa mutation frequency plot for all IGM sequences in
+the antigen selection tab.</span></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The data used to
+generate the aa mutation frequency plot for IGE:</span></u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>   Provides the
+data used to generate the aa mutation frequency plot for all IGE sequences in
+the antigen selection tab.</span></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Baseline PDF (</span></u><span
+lang=EN-GB><a href="http://selection.med.yale.edu/baseline/"><span
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>http://selection.med.yale.edu/baseline/</span></a></span><u><span
+lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'>):</span></u><span
+lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'> PDF
+containing the </span><span lang=EN-GB style='font-size:12.0pt;font-family:
+"Times New Roman","serif"'>Antigen selection (BASELINe) graph for all
+sequences.</span></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Baseline data:</span></u><span
+lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'>
+Table output of the BASELINe analysis. Calculation of antigen selection as
+performed by BASELINe are shown for each individual sequence and the sum of all
+sequences.</span></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Baseline IGA
+PDF:</span></u><span lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'>
+PDF containing the </span><span lang=EN-GB style='font-size:12.0pt;font-family:
+"Times New Roman","serif"'>Antigen selection (BASELINe) graph for all
+sequences.</span></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Baseline IGA
+data:</span></u><span lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'>
+Table output of the BASELINe analysis. Calculation of antigen selection as
+performed by BASELINe are shown for each individual IGA sequence and the sum of
+all IGA sequences.</span></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Baseline IGG
+PDF:</span></u><span lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'>
+PDF containing the </span><span lang=EN-GB style='font-size:12.0pt;font-family:
+"Times New Roman","serif"'>Antigen selection (BASELINe) graph for all IGG
+sequences.</span></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Baseline IGG
+data:</span></u><span lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'>
+Table output of the BASELINe analysis. Calculation of antigen selection as
+performed by BASELINe are shown for each individual IGG sequence and the sum of
+all IGG sequences.        </span></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Baseline IGM PDF:</span></u><span
+lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'> PDF
+containing the </span><span lang=EN-GB style='font-size:12.0pt;font-family:
+"Times New Roman","serif"'>Antigen selection (BASELINe) graph for all IGM
+sequences.</span></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Baseline IGM
+data:</span></u><span lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'>
+Table output of the BASELINe analysis. Calculation of antigen selection as
+performed by BASELINe are shown for each individual IGM sequence and the sum of
+all IGM sequences.</span></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Baseline IGE
+PDF:</span></u><span lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'>
+PDF containing the </span><span lang=EN-GB style='font-size:12.0pt;font-family:
+"Times New Roman","serif"'>Antigen selection (BASELINe) graph for all IGE
+sequences.</span><span lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'>
+</span></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Baseline IGE
+data:</span></u><span lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'>
+Table output of the BASELINe analysis. Calculation of antigen selection as
+performed by BASELINe are shown for each individual IGE sequence and the sum of
+all IGE sequences.</span></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><b><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>CSR</span></b></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The data for the
+</span></u><u><span lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'>IGA
+subclass distribution plot :</span></u><span lang=EN-GB style='font-size:12.0pt;
+font-family:"Times New Roman","serif"'> </span><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Data used for
+the generation of the </span><span lang=EN-GB style='font-size:12.0pt;
+font-family:"Times New Roman","serif"'>IGA subclass distribution plot provided
+in the CSR tab. </span></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The data for the
+</span></u><u><span lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'>IGA
+subclass distribution plot :</span></u><span lang=EN-GB style='font-size:12.0pt;
+font-family:"Times New Roman","serif"'> Data used for the generation of the </span><span
+lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'>IGG
+subclass distribution plot provided in the CSR tab. </span></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><b><span lang=NL
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Clonal relation</span></b></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Sequence overlap
+between subclasses:</span></u><span lang=EN-GB style='font-size:12.0pt;
+font-family:"Times New Roman","serif"'> Link to the overlap table as provided
+under the clonality overlap tab.         </span></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The Change-O DB
+file with defined clones and subclass annotation:</span></u><span
+lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'>
+Downloads a table with the calculation of clonal relation between all
+sequences. For each individual transcript the results of the clonal assignment
+as provided by Change-O are provided. Sequences with the same number in the CLONE
+column are considered clonally related. </span></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The Change-O DB
+defined clones summary file:</span></u><span lang=EN-GB style='font-size:12.0pt;
+font-family:"Times New Roman","serif"'> Gives a summary of the total number of
+clones in all sequences and their clone size.           </span></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The Change-O DB
+file with defined clones of IGA:</span></u><span lang=EN-GB style='font-size:
+12.0pt;font-family:"Times New Roman","serif"'> Downloads a table with the
+calculation of clonal relation between all IGA sequences. For each individual
+transcript the results of the clonal assignment as provided by Change-O are
+provided. Sequences with the same number in the CLONE column are considered
+clonally related. </span></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The Change-O DB
+defined clones summary file of IGA:</span></u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'> Gives a summary
+of the total number of clones in all IGA sequences and their clone size.</span></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The Change-O DB
+file with defined clones of IGG:</span></u><span lang=EN-GB style='font-size:
+12.0pt;font-family:"Times New Roman","serif"'> Downloads a table with the
+calculation of clonal relation between all IGG sequences. For each individual
+transcript the results of the clonal assignment as provided by Change-O are
+provided. Sequences with the same number in the CLONE column are considered
+clonally related. </span></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The Change-O DB
+defined clones summary file of IGG:</span></u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'> Gives a summary
+of the total number of clones in all IGG sequences and their clone size.</span></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The Change-O DB
+file with defined clones of IGM:</span></u><span lang=EN-GB style='font-size:
+12.0pt;font-family:"Times New Roman","serif"'> Downloads a table
+with the calculation of clonal relation between all IGM sequences. For each
+individual transcript the results of the clonal assignment as provided by
+Change-O are provided. Sequences with the same number in the CLONE column are
+considered clonally related. </span></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The Change-O DB
+defined clones summary file of IGM:</span></u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'> Gives a summary
+of the total number of clones in all IGM sequences and their clone size.</span></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The Change-O DB
+file with defined clones of IGE:</span></u><span lang=EN-GB style='font-size:
+12.0pt;font-family:"Times New Roman","serif"'> Downloads a table with the
+calculation of clonal relation between all IGE sequences. For each individual
+transcript the results of the clonal assignment as provided by Change-O are
+provided. Sequences with the same number in the CLONE column are considered
+clonally related. </span></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The Change-O DB
+defined clones summary file of IGE:</span></u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'> Gives a summary
+of the total number of clones in all IGE sequences and their clone size.</span></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><b><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Filtered IMGT
+output files</span></b></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>An IMGT archive
+with just the matched and filtered sequences:</span></u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'> Downloads a
+.txz file with the same format as downloaded IMGT files that contains all
+sequences that have passed the chosen filter settings.</span></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>An IMGT archive
+with just the matched and filtered IGA sequences:</span></u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'> Downloads a
+.txz file with the same format as downloaded IMGT files that contains all IGA
+sequences that have passed the chosen filter settings.</span></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>An IMGT archive
+with just the matched and filtered IGA1 sequences:</span></u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'> Downloads a
+.txz file with the same format as downloaded IMGT files that contains all IGA1
+sequences that have passed the chosen filter settings.</span></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>An IMGT archive
+with just the matched and filtered IGA2 sequences:</span></u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'> Downloads a .txz
+file with the same format as downloaded IMGT files that contains all IGA2
+sequences that have passed the chosen filter settings.</span></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>An IMGT archive
+with just the matched and filtered IGG sequences:</span></u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'> Downloads a .txz
+file with the same format as downloaded IMGT files that contains all IGG
+sequences that have passed the chosen filter settings.</span></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>An IMGT archive
+with just the matched and filtered IGG1 sequences:</span></u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'> Downloads a
+.txz file with the same format as downloaded IMGT files that contains all IGG1
+sequences that have passed the chosen filter settings.</span></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>An IMGT archive
+with just the matched and filtered IGG2 sequences:</span></u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'> Downloads a
+.txz file with the same format as downloaded IMGT files that contains all IGG2
+sequences that have passed the chosen filter settings.</span></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>An IMGT archive
+with just the matched and filtered IGG3 sequences:</span></u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'> Downloads a .txz
+file with the same format as downloaded IMGT files that contains all IGG3
+sequences that have passed the chosen filter settings.</span></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>An IMGT archive
+with just the matched and filtered IGG4 sequences:</span></u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'> Downloads a
+.txz file with the same format as downloaded IMGT files that contains all IGG4
+sequences that have passed the chosen filter settings.</span></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>An IMGT archive
+with just the matched and filtered IGM sequences:</span></u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'> Downloads a .txz
+file with the same format as downloaded IMGT files that contains all IGM
+sequences that have passed the chosen filter settings.</span></p>
+
+<p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'>An IMGT archive
+with just the matched and filtered IGE sequences:</span></u><span lang=EN-GB
+style='font-size:12.0pt;font-family:"Times New Roman","serif"'> Downloads a
+.txz file with the same format as downloaded IMGT files that contains all IGE
+sequences that have passed the chosen filter settings.</span></p>
+
+</div>
+
+</body>
+
+</html>