Mercurial > repos > davidvanzessen > shm_csr
annotate shm_selection.htm @ 98:d714f5ea83d7 draft default tip
planemo upload commit 1a01065a084a817382872154f779b94090a35ebf
| author | rhpvorderman |
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| date | Wed, 10 Jan 2024 12:32:47 +0000 |
| parents | 6809c63d9161 |
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| 67 | 1 <html> |
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4 <meta http-equiv=Content-Type content="text/html; charset=UTF-8"> |
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| 48 <div class=WordSection1> | |
| 49 | |
| 50 <p class=MsoNormalCxSpFirst style='text-align:justify'><b><span lang=EN-GB | |
| 51 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>References</span></b></p> | |
| 52 | |
| 53 <p class=MsoNormalCxSpMiddle style='text-align:justify'><span lang=EN-GB | |
| 54 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"; | |
| 55 color:black'>Yaari, G. and Uduman, M. and Kleinstein, S. H. (2012). Quantifying | |
| 56 selection in high-throughput Immunoglobulin sequencing data sets. In<span | |
| 57 class=apple-converted-space> </span><em>Nucleic Acids Research, 40 (17), | |
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58 pp. e134–e134.</em><span class=apple-converted-space><i> </i></span>[</span><span |
| 67 | 59 lang=EN-GB><a href="http://dx.doi.org/10.1093/nar/gks457" target="_blank"><span |
| 60 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"; | |
| 61 color:#303030'>doi:10.1093/nar/gks457</span></a></span><span lang=EN-GB | |
| 62 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"; | |
| 63 color:black'>][</span><span lang=EN-GB><a | |
| 64 href="http://dx.doi.org/10.1093/nar/gks457" target="_blank"><span | |
| 65 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"; | |
| 66 color:#303030'>Link</span></a></span><span lang=EN-GB style='font-size:12.0pt; | |
| 67 line-height:115%;font-family:"Times New Roman","serif";color:black'>]</span></p> | |
| 68 | |
| 69 <p class=MsoNormalCxSpMiddle style='text-align:justify'><b><span lang=EN-GB | |
| 70 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Graphs</span></b></p> | |
| 71 | |
| 72 <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span lang=EN-GB | |
| 73 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>AA | |
| 74 mutation frequency</span></u></p> | |
| 75 | |
| 76 <p class=MsoNormalCxSpMiddle style='text-align:justify'><span lang=EN-GB | |
| 77 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>For | |
| 78 each class, the frequency of replacement mutations at each amino acid position | |
| 79 is shown, which is calculated by dividing the number of replacement mutations | |
| 80 at a particular amino acid position/the number sequences that have an amino | |
| 81 acid at that particular position. Since the length of the CDR1 and CDR2 region | |
| 82 is not the same for every VH gene, some amino acids positions are absent. | |
| 83 Therefore we calculate the frequency using the number of amino acids present at | |
| 84 that that particular location. </span></p> | |
| 85 | |
| 86 <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span lang=EN-GB | |
| 87 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Antigen | |
| 88 selection (BASELINe)</span></u></p> | |
| 89 | |
| 90 <p class=MsoNormalCxSpMiddle style='text-align:justify'><span lang=EN-GB | |
| 91 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Shows | |
| 92 the results of the analysis of antigen selection as performed using BASELINe. | |
| 93 Details on the analysis performed by BASELINe can be found in Yaari et al, | |
| 94 PMID: 22641856. The settings used for the analysis are</span><span lang=EN-GB | |
| 95 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>: | |
| 96 focused, SHM targeting model: human Tri-nucleotide, custom bounderies. The | |
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"planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26"
rhpvorderman
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97 custom boundries are dependent on the ‘sequence starts at filter’. </span></p> |
| 67 | 98 |
| 99 <p class=MsoNormalCxSpMiddle style='line-height:normal'><span lang=NL | |
| 100 style='font-family:UICTFontTextStyleBody;color:black'>Leader: | |
| 101 1:26:38:55:65:104:-</span></p> | |
| 102 | |
| 103 <p class=MsoNormalCxSpMiddle style='line-height:normal'><span lang=NL | |
| 104 style='font-family:UICTFontTextStyleBody;color:black'>FR1: 27:27:38:55:65:104:-</span></p> | |
| 105 | |
| 106 <p class=MsoNormalCxSpMiddle style='line-height:normal'><span lang=NL | |
| 107 style='font-family:UICTFontTextStyleBody;color:black'>CDR1: 27:27:38:55:65:104:-</span></p> | |
| 108 | |
| 109 <p class=MsoNormalCxSpLast style='line-height:normal'><span lang=NL | |
| 110 style='font-family:UICTFontTextStyleBody;color:black'>FR2: 27:27:38:55:65:104:-</span></p> | |
| 111 | |
| 112 <p class=MsoNormal><span lang=NL style='font-size:12.0pt;line-height:115%; | |
| 113 font-family:"Times New Roman","serif"'>Hanna IJspeert, Pauline A. van | |
| 114 Schouwenburg, David van Zessen, Ingrid Pico-Knijnenburg, Gertjan J. Driessen, | |
| 115 Andrew P. Stubbs, and Mirjam van der Burg (2016). </span><span | |
| 116 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Evaluation | |
| 117 of the Antigen-Experienced B-Cell Receptor Repertoire in Healthy Children and | |
| 118 Adults. In <i>Frontiers in Immunolog, 7, pp. e410-410. </i>[<a | |
| 119 href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5066086/"><span | |
| 120 style='color:windowtext'>doi:10.3389/fimmu.2016.00410</span></a>][<a | |
| 121 href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5066086/"><span | |
| 122 style='color:windowtext'>Link</span></a>]</span></p> | |
| 123 | |
| 124 </div> | |
| 125 | |
| 126 </body> | |
| 127 | |
| 128 </html> |