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comparison shm_csr.htm @ 90:6809c63d9161 draft

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"planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26"
author rhpvorderman
date Tue, 25 Jan 2022 11:28:29 +0000
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89:3c9d4d976c47 90:6809c63d9161
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5 <meta name=Generator content="Microsoft Word 14 (filtered)"> 5 <meta name=Generator content="Microsoft Word 14 (filtered)">
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47 47
48 <p class=MsoNormalCxSpFirst style='text-align:justify'><span lang=EN-GB 48 <p class=MsoNormalCxSpFirst style='text-align:justify'><span lang=EN-GB
49 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The 49 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
50 graphs in this tab give insight into the subclass distribution of IGG and IGA 50 graphs in this tab give insight into the subclass distribution of IGG and IGA
51 transcripts. </span><span lang=EN-GB style='font-size:12.0pt;line-height:115%; 51 transcripts. </span><span lang=EN-GB style='font-size:12.0pt;line-height:115%;
52 font-family:"Times New Roman","serif"'>Human Cµ, C&#945;, C&#947; and C&#949; 52 font-family:"Times New Roman","serif"'>Human Cµ, C&#945;, C&#947; and C&#949;
53 constant genes are assigned using a </span><span lang=EN-GB style='font-size: 53 constant genes are assigned using a </span><span lang=EN-GB style='font-size:
54 12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>custom script 54 12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>custom script
55 specifically designed for human (sub)class assignment in repertoire data as 55 specifically designed for human (sub)class assignment in repertoire data as
56 described in van Schouwenburg and IJspeert et al, submitted for publication. In 56 described in van Schouwenburg and IJspeert et al, submitted for publication. In
57 this script the reference sequences for the subclasses are divided in 8 57 this script the reference sequences for the subclasses are divided in 8
58 nucleotide chunks which overlap by 4 nucleotides. These overlapping chunks are 58 nucleotide chunks which overlap by 4 nucleotides. These overlapping chunks are
59 then individually aligned in the right order to each input sequence. The 59 then individually aligned in the right order to each input sequence. The
60 percentage of the chunks identified in each rearrangement is calculated in the 60 percentage of the chunks identified in each rearrangement is calculated in the
61 ‘chunk hit percentage’. </span><span lang=EN-GB style='font-size:12.0pt; 61 ‘chunk hit percentage’. </span><span lang=EN-GB style='font-size:12.0pt;
62 line-height:115%;font-family:"Times New Roman","serif"'>C&#945; and C&#947; 62 line-height:115%;font-family:"Times New Roman","serif"'>C&#945; and C&#947;
63 subclasses are very homologous and only differ in a few nucleotides. To assign 63 subclasses are very homologous and only differ in a few nucleotides. To assign
64 subclasses the </span><span lang=EN-GB style='font-size:12.0pt;line-height: 64 subclasses the </span><span lang=EN-GB style='font-size:12.0pt;line-height:
65 115%;font-family:"Times New Roman","serif"'>‘nt hit percentage’ is calculated. 65 115%;font-family:"Times New Roman","serif"'>‘nt hit percentage’ is calculated.
66 This percentage indicates how well the chunks covering the subclass specific 66 This percentage indicates how well the chunks covering the subclass specific
67 nucleotide match with the different subclasses. </span><span lang=EN-GB 67 nucleotide match with the different subclasses. </span><span lang=EN-GB
68 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Information 68 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Information
69 on normal distribution of subclasses in healthy individuals of different ages 69 on normal distribution of subclasses in healthy individuals of different ages
70 can be found in IJspeert and van Schouwenburg et al, PMID: 27799928.</span></p> 70 can be found in IJspeert and van Schouwenburg et al, PMID: 27799928.</span></p>