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annotate shm_selection.htm @ 5:495a521cf9f2 draft

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"planemo upload commit 40d62ec3d2fea3c3bac605c976941e1f3b7e2cd4"
author rhpvorderman
date Tue, 16 Nov 2021 11:16:06 +0000
parents c8f02bce10d0
children
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1 <html>
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5 <meta name=Generator content="Microsoft Word 14 (filtered)">
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6 <style>
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7 <!--
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8 /* Font Definitions */
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10 {font-family:Calibri;
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11 panose-1:2 15 5 2 2 2 4 3 2 4;}
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13 {font-family:UICTFontTextStyleBody;}
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14 /* Style Definitions */
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15 p.MsoNormal, li.MsoNormal, div.MsoNormal
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16 {margin-top:0in;
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22 font-family:"Calibri","sans-serif";}
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23 a:link, span.MsoHyperlink
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27 {color:purple;
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31 .MsoChpDefault
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32 {font-family:"Calibri","sans-serif";}
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34 {margin-bottom:10.0pt;
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35 line-height:115%;}
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36 @page WordSection1
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37 {size:8.5in 11.0in;
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38 margin:1.0in 1.0in 1.0in 1.0in;}
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39 div.WordSection1
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40 {page:WordSection1;}
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41 -->
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42 </style>
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44 </head>
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46 <body lang=EN-US link=blue vlink=purple>
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48 <div class=WordSection1>
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49
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50 <p class=MsoNormalCxSpFirst style='text-align:justify'><b><span lang=EN-GB
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51 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>References</span></b></p>
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52
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53 <p class=MsoNormalCxSpMiddle style='text-align:justify'><span lang=EN-GB
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54 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif";
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55 color:black'>Yaari, G. and Uduman, M. and Kleinstein, S. H. (2012). Quantifying
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56 selection in high-throughput Immunoglobulin sequencing data sets. In<span
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57 class=apple-converted-space>&nbsp;</span><em>Nucleic Acids Research, 40 (17),
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58 pp. e134–e134.</em><span class=apple-converted-space><i>&nbsp;</i></span>[</span><span
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59 lang=EN-GB><a href="http://dx.doi.org/10.1093/nar/gks457" target="_blank"><span
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60 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif";
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61 color:#303030'>doi:10.1093/nar/gks457</span></a></span><span lang=EN-GB
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62 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif";
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63 color:black'>][</span><span lang=EN-GB><a
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64 href="http://dx.doi.org/10.1093/nar/gks457" target="_blank"><span
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65 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif";
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66 color:#303030'>Link</span></a></span><span lang=EN-GB style='font-size:12.0pt;
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67 line-height:115%;font-family:"Times New Roman","serif";color:black'>]</span></p>
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68
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69 <p class=MsoNormalCxSpMiddle style='text-align:justify'><b><span lang=EN-GB
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70 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Graphs</span></b></p>
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71
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72 <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span lang=EN-GB
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73 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>AA
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74 mutation frequency</span></u></p>
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75
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76 <p class=MsoNormalCxSpMiddle style='text-align:justify'><span lang=EN-GB
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77 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>For
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78 each class, the frequency of replacement mutations at each amino acid position
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79 is shown, which is calculated by dividing the number of replacement mutations
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80 at a particular amino acid position/the number sequences that have an amino
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81 acid at that particular position. Since the length of the CDR1 and CDR2 region
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82 is not the same for every VH gene, some amino acids positions are absent.
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83 Therefore we calculate the frequency using the number of amino acids present at
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84 that that particular location. </span></p>
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85
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86 <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span lang=EN-GB
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87 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Antigen
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88 selection (BASELINe)</span></u></p>
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89
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90 <p class=MsoNormalCxSpMiddle style='text-align:justify'><span lang=EN-GB
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91 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Shows
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92 the results of the analysis of antigen selection as performed using BASELINe.
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93 Details on the analysis performed by BASELINe can be found in Yaari et al,
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94 PMID: 22641856. The settings used for the analysis are</span><span lang=EN-GB
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95 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>:
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96 focused, SHM targeting model: human Tri-nucleotide, custom bounderies. The
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97 custom boundries are dependent on the ‘sequence starts at filter’. </span></p>
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98
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99 <p class=MsoNormalCxSpMiddle style='line-height:normal'><span lang=NL
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100 style='font-family:UICTFontTextStyleBody;color:black'>Leader:
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101 1:26:38:55:65:104:-</span></p>
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102
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103 <p class=MsoNormalCxSpMiddle style='line-height:normal'><span lang=NL
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104 style='font-family:UICTFontTextStyleBody;color:black'>FR1: 27:27:38:55:65:104:-</span></p>
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105
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106 <p class=MsoNormalCxSpMiddle style='line-height:normal'><span lang=NL
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107 style='font-family:UICTFontTextStyleBody;color:black'>CDR1:&nbsp;27:27:38:55:65:104:-</span></p>
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108
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109 <p class=MsoNormalCxSpLast style='line-height:normal'><span lang=NL
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110 style='font-family:UICTFontTextStyleBody;color:black'>FR2:&nbsp;27:27:38:55:65:104:-</span></p>
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111
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112 <p class=MsoNormal><span lang=NL style='font-size:12.0pt;line-height:115%;
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113 font-family:"Times New Roman","serif"'>Hanna IJspeert, Pauline A. van
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114 Schouwenburg, David van Zessen, Ingrid Pico-Knijnenburg, Gertjan J. Driessen,
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115 Andrew P. Stubbs, and Mirjam van der Burg (2016). </span><span
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116 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Evaluation
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117 of the Antigen-Experienced B-Cell Receptor Repertoire in Healthy Children and
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118 Adults. In <i>Frontiers in Immunolog, 7, pp. e410-410. </i>[<a
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119 href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5066086/"><span
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120 style='color:windowtext'>doi:10.3389/fimmu.2016.00410</span></a>][<a
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121 href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5066086/"><span
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122 style='color:windowtext'>Link</span></a>]</span></p>
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123
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124 </div>
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125
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126 </body>
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127
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128 </html>