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date Thu, 22 Dec 2016 09:39:27 -0500
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2
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79 <div class=WordSection1>
80
81 <p style='margin-top:0in;margin-right:0in;margin-bottom:6.4pt;margin-left:0in;
82 text-align:justify;background:white'><b><span lang=EN-GB style='color:black'>References</span></b></p>
83
84 <p style='margin-top:0in;margin-right:0in;margin-bottom:6.4pt;margin-left:0in;
85 text-align:justify;background:white'><span lang=EN-GB style='color:black'>Gupta,
86 Namita T. and Vander Heiden, Jason A. and Uduman, Mohamed and Gadala-Maria,
87 Daniel and Yaari, Gur and Kleinstein, Steven H. (2015). <a name="OLE_LINK106"></a><a
88 name="OLE_LINK107"></a>Change-O: a toolkit for analyzing large-scale B cell
89 immunoglobulin repertoire sequencing data: Table 1. In<span
90 class=apple-converted-space>&nbsp;</span><em>Bioinformatics, 31 (20), pp.
91 3356–3358.</em><span class=apple-converted-space><i>&nbsp;</i></span>[</span><a
92 href="http://dx.doi.org/10.1093/bioinformatics/btv359" target="_blank"><span
93 lang=EN-GB style='color:#303030'>doi:10.1093/bioinformatics/btv359</span></a><span
94 lang=EN-GB style='color:black'>][</span><a
95 href="http://dx.doi.org/10.1093/bioinformatics/btv359" target="_blank"><span
96 lang=EN-GB style='color:#303030'>Link</span></a><span lang=EN-GB
97 style='color:black'>]</span></p>
98
99 <p style='margin-top:0in;margin-right:0in;margin-bottom:6.4pt;margin-left:0in;
100 text-align:justify;background:white'><span lang=EN-GB style='color:black'>&nbsp;</span></p>
101
102 <p style='margin-top:0in;margin-right:0in;margin-bottom:6.4pt;margin-left:0in;
103 text-align:justify;background:white'><a name="OLE_LINK110"><u><span lang=EN-GB
104 style='color:black'>All, IGA, IGG, IGM and IGE tabs</span></u></a></p>
105
106 <p style='margin-top:0in;margin-right:0in;margin-bottom:6.4pt;margin-left:0in;
107 text-align:justify;background:white'><span lang=EN-GB style='color:black'>In
108 these tabs information on the clonal relation of transcripts can be found. To
109 calculate clonal relation Change-O is used (Gupta et al, PMID: 26069265).
110 Transcripts are considered clonally related if they have maximal three nucleotides
111 difference in their CDR3 sequence and the same first V segment (as assigned by
112 IMGT). Results are represented in a table format showing the clone size and the
113 number of clones or sequences with this clone size. Change-O settings used are
114 the </span><span lang=EN-GB>nucleotide hamming distance substitution model with
115 a complete distance of maximal three. For clonal assignment the first gene
116 segments were used, and the distances were not normalized. In case of
117 asymmetric distances, the minimal distance was used.<span style='color:black'> </span></span></p>
118
119 <p style='margin-top:0in;margin-right:0in;margin-bottom:6.4pt;margin-left:0in;
120 text-align:justify;background:white'><span lang=EN-GB style='color:black'>&nbsp;</span></p>
121
122 <p style='margin-top:0in;margin-right:0in;margin-bottom:6.4pt;margin-left:0in;
123 text-align:justify;background:white'><u><span lang=EN-GB style='color:black'>Overlap
124 tab</span></u><span lang=EN-GB style='color:black'> </span></p>
125
126 <p style='margin-top:0in;margin-right:0in;margin-bottom:6.4pt;margin-left:0in;
127 text-align:justify;background:white'><span lang=EN-GB style='color:black'>This
128 tab gives information on with which (sub)classe(s) each unique analyzed region
129 (based on the exact nucleotide sequence of the analyzes region and the CDR3
130 nucleotide sequence) is found with. This gives information if the combination
131 of the exact same nucleotide sequence of the analyzed region and the CDR3
132 sequence can be found in multiple (sub)classes.</span></p>
133
134 <p style='margin-top:0in;margin-right:0in;margin-bottom:6.4pt;margin-left:0in;
135 text-align:justify;background:white'><span style='color:black'><img src="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAA8AAAAPCAYAAAA71pVKAAAAzElEQVQoka2TwQ2CQBBFpwTshw4ImW8ogJMlUIMmhNCDxgasAi50oSXA8XlAjCG7aqKTzGX/vsnM31mzR0gk7tTudO5MEizpzvQ4ryUSe408J3Xn+grE0p1rnpOamVmWsZG4rS+dzzAMsN8Hi9yyjI1JNGtxu4VxBJgLRLpoTKIPiW0LlwtUVRTubW2OBGUJu92cZRmdfbKQMAw8o+vi5v0fLorZ7Y9waGYJjsf38DJz0O1PsEQffOcv4Sa6YYfDDJ5Obzbsp93+5VfdATueO1fdLdI0AAAAAElFTkSuQmCC"> Please note that this tab is based on all
136 sequences before filter unique sequences and the remove duplicates based on
137 filters are applied. In this table only sequences according more than once are
138 included. </span></p>
139
140 </div>
141
142 </body>
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