Mercurial > repos > davidvanzessen > shm_csr
annotate shm_downloads.htm @ 97:fbc6307dd83b draft
planemo upload commit 91fd26f19cb20fc2ee4d87d7edbc9ce6099752b0
| author | rhpvorderman |
|---|---|
| date | Mon, 08 Jan 2024 08:50:07 +0000 |
| parents | 6809c63d9161 |
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| rev | line source |
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| 67 | 1 <html> |
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| 3 <head> | |
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4 <meta http-equiv=Content-Type content="text/html; charset=UTF-8"> |
| 67 | 5 <meta name=Generator content="Microsoft Word 14 (filtered)"> |
| 6 <style> | |
| 7 <!-- | |
| 8 /* Font Definitions */ | |
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| 11 panose-1:2 15 5 2 2 2 4 3 2 4;} | |
| 12 /* Style Definitions */ | |
| 13 p.MsoNormal, li.MsoNormal, div.MsoNormal | |
| 14 {margin-top:0in; | |
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| 20 font-family:"Calibri","sans-serif";} | |
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| 23 text-decoration:underline;} | |
| 24 a:visited, span.MsoHyperlinkFollowed | |
| 25 {color:purple; | |
| 26 text-decoration:underline;} | |
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| 30 font-size:11.0pt; | |
| 31 font-family:"Calibri","sans-serif";} | |
| 32 .MsoChpDefault | |
| 33 {font-family:"Calibri","sans-serif";} | |
| 34 .MsoPapDefault | |
| 35 {margin-bottom:10.0pt; | |
| 36 line-height:115%;} | |
| 37 @page WordSection1 | |
| 38 {size:8.5in 11.0in; | |
| 39 margin:1.0in 1.0in 1.0in 1.0in;} | |
| 40 div.WordSection1 | |
| 41 {page:WordSection1;} | |
| 42 --> | |
| 43 </style> | |
| 44 | |
| 45 </head> | |
| 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 | |
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80 table as a data set. </span></p> |
| 67 | 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), | |
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100 the assigned subclass and the number of sequenced A,C,G and T’s.</span></p> |
| 67 | 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 | |
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138 SHM frequency tab. </span></p> |
| 67 | 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 >20% SHM. Information is provided for each subclass.</span></p> | |
| 146 | |
| 147 <p class=MsoNoSpacing style='text-align:justify'><span lang=EN-GB | |
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148 style='font-size:12.0pt;font-family:"Times New Roman","serif"'> </span></p> |
| 67 | 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 | |
|
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"planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26"
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parents:
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changeset
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270 style='font-size:12.0pt;font-family:"Times New Roman","serif"'> Provides the |
| 67 | 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 | |
|
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"planemo upload commit fd64827ff6e63df008f6f50ddb8576ad2b1dbb26"
rhpvorderman
parents:
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changeset
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317 all IGG sequences. </span></p> |
| 67 | 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 | |
|
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376 under the clonality overlap tab. </span></p> |
| 67 | 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 | |
|
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391 clones in all sequences and their clone size. </span></p> |
| 67 | 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: | |
|
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426 12.0pt;font-family:"Times New Roman","serif"'> Downloads a table |
| 67 | 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> |