Mercurial > repos > davidvanzessen > shm_csr
diff shm_downloads.htm @ 67:ba33b94637ca draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Tue, 29 Jan 2019 03:54:09 -0500 |
| parents | a24f8c93583a |
| children | 6809c63d9161 |
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--- a/shm_downloads.htm Thu Dec 07 03:44:38 2017 -0500 +++ b/shm_downloads.htm Tue Jan 29 03:54:09 2019 -0500 @@ -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%, ->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%, +>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>