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46
47 <body lang=EN-US link=blue vlink=purple>
48
49 <div class=WordSection1>
50
51 <p class=MsoNoSpacing style='text-align:justify'><b><span lang=EN-GB
52 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Info</span></b></p>
53
54 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
55 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The complete
56 dataset:</span></u><span lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'>
57 Allows downloading of the complete parsed data set.</span></p>
58
59 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
60 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The filtered
61 dataset:</span></u><span lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'>
62 Allows downloading of all parsed IMGT information of all transcripts that
63 passed the chosen filter settings.</span></p>
64
65 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
66 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The alignment
67 info on the unmatched sequences:</span></u><span lang=EN-GB style='font-size:
68 12.0pt;font-family:"Times New Roman","serif"'> Provides information of the subclass
69 alignment of all unmatched sequences. For each sequence the chunck hit
70 percentage and the nt hit percentage is shown together with the best matched
71 subclass.</span></p>
72
73 <p class=MsoNoSpacing style='text-align:justify'><b><span lang=EN-GB
74 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>SHM Overview</span></b></p>
75
76 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
77 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The SHM Overview
78 table as a dataset:</span></u><span lang=EN-GB style='font-size:12.0pt;
79 font-family:"Times New Roman","serif"'> Allows downloading of the SHM Overview
80 table as a data set.  </span></p>
81
82 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
83 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Motif data per
84 sequence ID:</span></u><span lang=EN-GB style='font-size:12.0pt;font-family:
85 "Times New Roman","serif"'> Provides a file that contains information for each
86 transcript on the number of mutations present in WA/TW and RGYW/WRCY motives.</span></p>
87
88 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
89 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Mutation data
90 per sequence ID: </span></u><span lang=EN-GB style='font-size:12.0pt;
91 font-family:"Times New Roman","serif"'>Provides a file containing information
92 on the number of sequences bases, the number and location of mutations and the
93 type of mutations found in each transcript. </span></p>
94
95 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
96 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Base count for
97 every sequence:</span></u><span lang=EN-GB style='font-size:12.0pt;font-family:
98 "Times New Roman","serif"'> links to a page showing for each transcript the
99 sequence of the analysed region (as dependent on the sequence starts at filter),
100 the assigned subclass and the number of sequenced A,C,G and T’s.</span></p>
101
102 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
103 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The data used to
104 generate the percentage of mutations in AID and pol eta motives plot:</span></u><span
105 lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'>
106 Provides a file containing the values used to generate the percentage of
107 mutations in AID and pol eta motives plot in the SHM overview tab.</span></p>
108
109 <p class=MsoNormalCxSpFirst style='text-align:justify'><u><span lang=EN-GB
110 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
111 data used to generate the relative mutation patterns plot:</span></u><span
112 lang=EN-GB style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
113 Provides a download with the data used to generate the relative mutation
114 patterns plot in the SHM overview tab.</span></p>
115
116 <p class=MsoNormalCxSpLast style='text-align:justify'><u><span lang=EN-GB
117 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
118 data used to generate the absolute mutation patterns plot:</span></u><span
119 lang=EN-GB style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
120 Provides a download with the data used to generate the absolute mutation
121 patterns plot in the SHM overview tab. </span></p>
122
123 <p class=MsoNoSpacing style='text-align:justify'><b><span lang=EN-GB
124 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>SHM Frequency</span></b></p>
125
126 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
127 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The data
128 generate the frequency scatter plot:</span></u><span lang=EN-GB
129 style='font-size:12.0pt;font-family:"Times New Roman","serif"'> Allows
130 downloading the data used to generate the frequency scatter plot in the SHM
131 frequency tab. </span></p>
132
133 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
134 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The data used to
135 generate the frequency by class plot:</span></u><span lang=EN-GB
136 style='font-size:12.0pt;font-family:"Times New Roman","serif"'> Allows
137 downloading the data used to generate frequency by class plot included in the
138 SHM frequency tab.           </span></p>
139
140 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
141 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The data for
142 frequency by subclass:</span></u><span lang=EN-GB style='font-size:12.0pt;
143 font-family:"Times New Roman","serif"'> Provides information of the number and
144 percentage of sequences that have 0%, 0-2%, 2-5%, 5-10%, 10-15%, 15-20%,
145 &gt;20% SHM. Information is provided for each subclass.</span></p>
146
147 <p class=MsoNoSpacing style='text-align:justify'><span lang=EN-GB
148 style='font-size:12.0pt;font-family:"Times New Roman","serif"'> </span></p>
149
150 <p class=MsoNoSpacing style='text-align:justify'><b><span lang=EN-GB
151 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Transition
152 Tables</span></b></p>
153
154 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
155 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The data for the
156 'all' transition plot:</span></u><span lang=EN-GB style='font-size:12.0pt;
157 font-family:"Times New Roman","serif"'> Contains the information used to
158 generate the transition table for all sequences.</span></p>
159
160 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
161 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The data for the
162 'IGA' transition plot:</span></u><span lang=EN-GB style='font-size:12.0pt;
163 font-family:"Times New Roman","serif"'> Contains the information used to
164 generate the transition table for all IGA sequences.</span></p>
165
166 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
167 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The data for the
168 'IGA1' transition plot:</span></u><span lang=EN-GB style='font-size:12.0pt;
169 font-family:"Times New Roman","serif"'> Contains the information used to
170 generate the transition table for all IGA1 sequences.</span></p>
171
172 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
173 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The data for the
174 'IGA2' transition plot:</span></u><span lang=EN-GB style='font-size:12.0pt;
175 font-family:"Times New Roman","serif"'> Contains the information used to
176 generate the transition table for all IGA2 sequences.</span></p>
177
178 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
179 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The data for the
180 'IGG' transition plot :</span></u><span lang=EN-GB style='font-size:12.0pt;
181 font-family:"Times New Roman","serif"'> Contains the information used to
182 generate the transition table for all IGG sequences.</span></p>
183
184 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
185 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The data for the
186 'IGG1' transition plot:</span></u><span lang=EN-GB style='font-size:12.0pt;
187 font-family:"Times New Roman","serif"'> Contains the information used to
188 generate the transition table for all IGG1 sequences.</span></p>
189
190 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
191 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The data for the
192 'IGG2' transition plot:</span></u><span lang=EN-GB style='font-size:12.0pt;
193 font-family:"Times New Roman","serif"'> Contains the information used to
194 generate the transition table for all IGG2 sequences.</span></p>
195
196 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
197 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The data for the
198 'IGG3' transition plot:</span></u><span lang=EN-GB style='font-size:12.0pt;
199 font-family:"Times New Roman","serif"'> Contains the information used to
200 generate the transition table for all IGG3 sequences.</span></p>
201
202 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
203 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The data for the
204 'IGG4' transition plot:</span></u><span lang=EN-GB style='font-size:12.0pt;
205 font-family:"Times New Roman","serif"'> Contains the information used to
206 generate the transition table for all IGG4 sequences.</span></p>
207
208 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
209 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The data for the
210 'IGM' transition plot :</span></u><span lang=EN-GB style='font-size:12.0pt;
211 font-family:"Times New Roman","serif"'> Contains the information used to
212 generate the transition table for all IGM sequences.</span></p>
213
214 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
215 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The data for the
216 'IGE' transition plot:</span></u><span lang=EN-GB style='font-size:12.0pt;
217 font-family:"Times New Roman","serif"'> Contains the
218 information used to generate the transition table for all IGE sequences.</span></p>
219
220 <p class=MsoNoSpacing style='text-align:justify'><b><span lang=EN-GB
221 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Antigen
222 selection</span></b></p>
223
224 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
225 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>AA mutation data
226 per sequence ID:</span></u><span lang=EN-GB style='font-size:12.0pt;font-family:
227 "Times New Roman","serif"'> Provides for each transcript information on whether
228 there is replacement mutation at each amino acid location (as defined by IMGT).
229 For all amino acids outside of the analysed region the value 0 is given.</span></p>
230
231 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
232 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Presence of AA
233 per sequence ID:</span></u><span lang=EN-GB style='font-size:12.0pt;font-family:
234 "Times New Roman","serif"'> Provides for each transcript information on which
235 amino acid location (as defined by IMGT) is present. </span><span lang=NL
236 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>0 is absent, 1
237 is present. </span></p>
238
239 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
240 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The data used to
241 generate the aa mutation frequency plot:</span></u><span lang=EN-GB
242 style='font-size:12.0pt;font-family:"Times New Roman","serif"'> Provides the
243 data used to generate the aa mutation frequency plot for all sequences in the
244 antigen selection tab.</span></p>
245
246 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
247 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The data used to
248 generate the aa mutation frequency plot for IGA:</span></u><span lang=EN-GB
249 style='font-size:12.0pt;font-family:"Times New Roman","serif"'> Provides the
250 data used to generate the aa mutation frequency plot for all IGA sequences in
251 the antigen selection tab.</span></p>
252
253 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
254 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The data used to
255 generate the aa mutation frequency plot for IGG:</span></u><span lang=EN-GB
256 style='font-size:12.0pt;font-family:"Times New Roman","serif"'> Provides the
257 data used to generate the aa mutation frequency plot for all IGG sequences in
258 the antigen selection tab.</span></p>
259
260 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
261 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The data used to
262 generate the aa mutation frequency plot for IGM:</span></u><span lang=EN-GB
263 style='font-size:12.0pt;font-family:"Times New Roman","serif"'> Provides the
264 data used to generate the aa mutation frequency plot for all IGM sequences in
265 the antigen selection tab.</span></p>
266
267 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
268 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The data used to
269 generate the aa mutation frequency plot for IGE:</span></u><span lang=EN-GB
270 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>  Provides the
271 data used to generate the aa mutation frequency plot for all IGE sequences in
272 the antigen selection tab.</span></p>
273
274 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
275 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Baseline PDF (</span></u><span
276 lang=EN-GB><a href="http://selection.med.yale.edu/baseline/"><span
277 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>http://selection.med.yale.edu/baseline/</span></a></span><u><span
278 lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'>):</span></u><span
279 lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'> PDF
280 containing the </span><span lang=EN-GB style='font-size:12.0pt;font-family:
281 "Times New Roman","serif"'>Antigen selection (BASELINe) graph for all
282 sequences.</span></p>
283
284 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
285 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Baseline data:</span></u><span
286 lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'>
287 Table output of the BASELINe analysis. Calculation of antigen selection as
288 performed by BASELINe are shown for each individual sequence and the sum of all
289 sequences.</span></p>
290
291 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
292 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Baseline IGA
293 PDF:</span></u><span lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'>
294 PDF containing the </span><span lang=EN-GB style='font-size:12.0pt;font-family:
295 "Times New Roman","serif"'>Antigen selection (BASELINe) graph for all
296 sequences.</span></p>
297
298 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
299 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Baseline IGA
300 data:</span></u><span lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'>
301 Table output of the BASELINe analysis. Calculation of antigen selection as
302 performed by BASELINe are shown for each individual IGA sequence and the sum of
303 all IGA sequences.</span></p>
304
305 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
306 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Baseline IGG
307 PDF:</span></u><span lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'>
308 PDF containing the </span><span lang=EN-GB style='font-size:12.0pt;font-family:
309 "Times New Roman","serif"'>Antigen selection (BASELINe) graph for all IGG
310 sequences.</span></p>
311
312 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
313 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Baseline IGG
314 data:</span></u><span lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'>
315 Table output of the BASELINe analysis. Calculation of antigen selection as
316 performed by BASELINe are shown for each individual IGG sequence and the sum of
317 all IGG sequences.        </span></p>
318
319 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
320 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Baseline IGM PDF:</span></u><span
321 lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'> PDF
322 containing the </span><span lang=EN-GB style='font-size:12.0pt;font-family:
323 "Times New Roman","serif"'>Antigen selection (BASELINe) graph for all IGM
324 sequences.</span></p>
325
326 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
327 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Baseline IGM
328 data:</span></u><span lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'>
329 Table output of the BASELINe analysis. Calculation of antigen selection as
330 performed by BASELINe are shown for each individual IGM sequence and the sum of
331 all IGM sequences.</span></p>
332
333 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
334 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Baseline IGE
335 PDF:</span></u><span lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'>
336 PDF containing the </span><span lang=EN-GB style='font-size:12.0pt;font-family:
337 "Times New Roman","serif"'>Antigen selection (BASELINe) graph for all IGE
338 sequences.</span><span lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'>
339 </span></p>
340
341 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
342 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Baseline IGE
343 data:</span></u><span lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'>
344 Table output of the BASELINe analysis. Calculation of antigen selection as
345 performed by BASELINe are shown for each individual IGE sequence and the sum of
346 all IGE sequences.</span></p>
347
348 <p class=MsoNoSpacing style='text-align:justify'><b><span lang=EN-GB
349 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>CSR</span></b></p>
350
351 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
352 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The data for the
353 </span></u><u><span lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'>IGA
354 subclass distribution plot :</span></u><span lang=EN-GB style='font-size:12.0pt;
355 font-family:"Times New Roman","serif"'> </span><span lang=EN-GB
356 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Data used for
357 the generation of the </span><span lang=EN-GB style='font-size:12.0pt;
358 font-family:"Times New Roman","serif"'>IGA subclass distribution plot provided
359 in the CSR tab. </span></p>
360
361 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
362 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The data for the
363 </span></u><u><span lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'>IGA
364 subclass distribution plot :</span></u><span lang=EN-GB style='font-size:12.0pt;
365 font-family:"Times New Roman","serif"'> Data used for the generation of the </span><span
366 lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'>IGG
367 subclass distribution plot provided in the CSR tab. </span></p>
368
369 <p class=MsoNoSpacing style='text-align:justify'><b><span lang=NL
370 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Clonal relation</span></b></p>
371
372 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
373 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Sequence overlap
374 between subclasses:</span></u><span lang=EN-GB style='font-size:12.0pt;
375 font-family:"Times New Roman","serif"'> Link to the overlap table as provided
376 under the clonality overlap tab.         </span></p>
377
378 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
379 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The Change-O DB
380 file with defined clones and subclass annotation:</span></u><span
381 lang=EN-GB style='font-size:12.0pt;font-family:"Times New Roman","serif"'>
382 Downloads a table with the calculation of clonal relation between all
383 sequences. For each individual transcript the results of the clonal assignment
384 as provided by Change-O are provided. Sequences with the same number in the CLONE
385 column are considered clonally related. </span></p>
386
387 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
388 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The Change-O DB
389 defined clones summary file:</span></u><span lang=EN-GB style='font-size:12.0pt;
390 font-family:"Times New Roman","serif"'> Gives a summary of the total number of
391 clones in all sequences and their clone size.           </span></p>
392
393 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
394 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The Change-O DB
395 file with defined clones of IGA:</span></u><span lang=EN-GB style='font-size:
396 12.0pt;font-family:"Times New Roman","serif"'> Downloads a table with the
397 calculation of clonal relation between all IGA sequences. For each individual
398 transcript the results of the clonal assignment as provided by Change-O are
399 provided. Sequences with the same number in the CLONE column are considered
400 clonally related. </span></p>
401
402 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
403 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The Change-O DB
404 defined clones summary file of IGA:</span></u><span lang=EN-GB
405 style='font-size:12.0pt;font-family:"Times New Roman","serif"'> Gives a summary
406 of the total number of clones in all IGA sequences and their clone size.</span></p>
407
408 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
409 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The Change-O DB
410 file with defined clones of IGG:</span></u><span lang=EN-GB style='font-size:
411 12.0pt;font-family:"Times New Roman","serif"'> Downloads a table with the
412 calculation of clonal relation between all IGG sequences. For each individual
413 transcript the results of the clonal assignment as provided by Change-O are
414 provided. Sequences with the same number in the CLONE column are considered
415 clonally related. </span></p>
416
417 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
418 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The Change-O DB
419 defined clones summary file of IGG:</span></u><span lang=EN-GB
420 style='font-size:12.0pt;font-family:"Times New Roman","serif"'> Gives a summary
421 of the total number of clones in all IGG sequences and their clone size.</span></p>
422
423 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
424 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The Change-O DB
425 file with defined clones of IGM:</span></u><span lang=EN-GB style='font-size:
426 12.0pt;font-family:"Times New Roman","serif"'> Downloads a table
427 with the calculation of clonal relation between all IGM sequences. For each
428 individual transcript the results of the clonal assignment as provided by
429 Change-O are provided. Sequences with the same number in the CLONE column are
430 considered clonally related. </span></p>
431
432 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
433 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The Change-O DB
434 defined clones summary file of IGM:</span></u><span lang=EN-GB
435 style='font-size:12.0pt;font-family:"Times New Roman","serif"'> Gives a summary
436 of the total number of clones in all IGM sequences and their clone size.</span></p>
437
438 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
439 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The Change-O DB
440 file with defined clones of IGE:</span></u><span lang=EN-GB style='font-size:
441 12.0pt;font-family:"Times New Roman","serif"'> Downloads a table with the
442 calculation of clonal relation between all IGE sequences. For each individual
443 transcript the results of the clonal assignment as provided by Change-O are
444 provided. Sequences with the same number in the CLONE column are considered
445 clonally related. </span></p>
446
447 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
448 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>The Change-O DB
449 defined clones summary file of IGE:</span></u><span lang=EN-GB
450 style='font-size:12.0pt;font-family:"Times New Roman","serif"'> Gives a summary
451 of the total number of clones in all IGE sequences and their clone size.</span></p>
452
453 <p class=MsoNoSpacing style='text-align:justify'><b><span lang=EN-GB
454 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>Filtered IMGT
455 output files</span></b></p>
456
457 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
458 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>An IMGT archive
459 with just the matched and filtered sequences:</span></u><span lang=EN-GB
460 style='font-size:12.0pt;font-family:"Times New Roman","serif"'> Downloads a
461 .txz file with the same format as downloaded IMGT files that contains all
462 sequences that have passed the chosen filter settings.</span></p>
463
464 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
465 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>An IMGT archive
466 with just the matched and filtered IGA sequences:</span></u><span lang=EN-GB
467 style='font-size:12.0pt;font-family:"Times New Roman","serif"'> Downloads a
468 .txz file with the same format as downloaded IMGT files that contains all IGA
469 sequences that have passed the chosen filter settings.</span></p>
470
471 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
472 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>An IMGT archive
473 with just the matched and filtered IGA1 sequences:</span></u><span lang=EN-GB
474 style='font-size:12.0pt;font-family:"Times New Roman","serif"'> Downloads a
475 .txz file with the same format as downloaded IMGT files that contains all IGA1
476 sequences that have passed the chosen filter settings.</span></p>
477
478 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
479 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>An IMGT archive
480 with just the matched and filtered IGA2 sequences:</span></u><span lang=EN-GB
481 style='font-size:12.0pt;font-family:"Times New Roman","serif"'> Downloads a .txz
482 file with the same format as downloaded IMGT files that contains all IGA2
483 sequences that have passed the chosen filter settings.</span></p>
484
485 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
486 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>An IMGT archive
487 with just the matched and filtered IGG sequences:</span></u><span lang=EN-GB
488 style='font-size:12.0pt;font-family:"Times New Roman","serif"'> Downloads a .txz
489 file with the same format as downloaded IMGT files that contains all IGG
490 sequences that have passed the chosen filter settings.</span></p>
491
492 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
493 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>An IMGT archive
494 with just the matched and filtered IGG1 sequences:</span></u><span lang=EN-GB
495 style='font-size:12.0pt;font-family:"Times New Roman","serif"'> Downloads a
496 .txz file with the same format as downloaded IMGT files that contains all IGG1
497 sequences that have passed the chosen filter settings.</span></p>
498
499 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
500 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>An IMGT archive
501 with just the matched and filtered IGG2 sequences:</span></u><span lang=EN-GB
502 style='font-size:12.0pt;font-family:"Times New Roman","serif"'> Downloads a
503 .txz file with the same format as downloaded IMGT files that contains all IGG2
504 sequences that have passed the chosen filter settings.</span></p>
505
506 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
507 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>An IMGT archive
508 with just the matched and filtered IGG3 sequences:</span></u><span lang=EN-GB
509 style='font-size:12.0pt;font-family:"Times New Roman","serif"'> Downloads a .txz
510 file with the same format as downloaded IMGT files that contains all IGG3
511 sequences that have passed the chosen filter settings.</span></p>
512
513 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
514 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>An IMGT archive
515 with just the matched and filtered IGG4 sequences:</span></u><span lang=EN-GB
516 style='font-size:12.0pt;font-family:"Times New Roman","serif"'> Downloads a
517 .txz file with the same format as downloaded IMGT files that contains all IGG4
518 sequences that have passed the chosen filter settings.</span></p>
519
520 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
521 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>An IMGT archive
522 with just the matched and filtered IGM sequences:</span></u><span lang=EN-GB
523 style='font-size:12.0pt;font-family:"Times New Roman","serif"'> Downloads a .txz
524 file with the same format as downloaded IMGT files that contains all IGM
525 sequences that have passed the chosen filter settings.</span></p>
526
527 <p class=MsoNoSpacing style='text-align:justify'><u><span lang=EN-GB
528 style='font-size:12.0pt;font-family:"Times New Roman","serif"'>An IMGT archive
529 with just the matched and filtered IGE sequences:</span></u><span lang=EN-GB
530 style='font-size:12.0pt;font-family:"Times New Roman","serif"'> Downloads a
531 .txz file with the same format as downloaded IMGT files that contains all IGE
532 sequences that have passed the chosen filter settings.</span></p>
533
534 </div>
535
536 </body>
537
538 </html>