Skip to main content

Table 1 Drug-target genes and high similarity initial-assembly contigs at multiple k-mers

From: Computational cloning of drug target genes of a parasitic nematode, Oesophagostomum dentatum

C. elegansTarget gene 21-mer HSPs 23-mer HSPs 25-mer HSPs 27-mer HSPs
ID Acc # CDS len # X ¯ R # X ¯ R # X ¯ R # X ¯ R
lev-1 CAB03148 1419 3 148 99-219 3 238 174-294 5 238 96-525 4 237 114-381
lev-8 CAB01685 1596 2 147 126-168 1 255 255 1 108 108   nd nd
unc-29 CAB02308 1482 12 144 105-168 7 259 120-480 8 248 132-426 11 202 96-402
unc-38 CCD69819 1524 6 180 111-294 9 184 90-375 9 283 84-1098 8 339 87-1380
unc-63 CCD66192 1524 3 272 105-576 5 247 96-510 5 263 105-510 5 235 105-510
avr-14 CCD61323 1251 1 90 90 2 112 102-123 2 114 105-123 4 111 105-123
avr-15 CAB03329 1437 4 163 123-210 7 154 123-192 6 140 105-210 3 185 123-240
ben-1 CAB00853 1335 2 163 108-219 1 111 111 1 114 114 3 102 90-117
glc-1 CAB07361 1305 1 123 123 1 108 108 1 318 318 1 237 237
glc-2 CCD62432 1305 4 198 147-318 1 879 879 1 939 939 3 375 207-582
glc-3 CCD69051 1455 3 146 87-207 2 115 111-120 2 102 93-111 4 117 99-144
glc-4 CCD65896 1503 6 192 111-279 2 702 249-1155 2 702 249-1155 2 702 249-1155
  29-mer HSPs 31-mer HSPs 33-mer HSPs 35-mer HSPs 37-mer HSPs
ID # X ¯ R # X ¯ R # X ¯ R # X ¯ R # X ¯ R
lev-1 5 219 93-420 11 150 99-330 9 181 114-255 8 207 102-558 6 334 138-657
lev-8    nd    nd    nd    nd    nd
unc-29 8 223 120-465 9 171 96-378 8 180 96-396 2 172 162-183 4 173 144-207
unc-38 7 493 90-1473 7 416 84-1473 6 472 108-1473 4 708 261-1473 3 890 360-1473
unc-63 3 227 105-297 4 285 105-414 3 275 105-414 1 414 414 2 277 141-414
avr-14 3 123 111-135 5 145 111-207 6 169 123-270 5 202 123-321 5 240 123-327
avr-15 5 156 90-243 7 153 96-291 4 132 93-213 4 138 96-243 4 108 108-111
ben-1 2 97 93-102 4 99 90-120 3 99 96-102 3 109 87-135 5 109 93-129
glc-1 1 237 237    nd 2 141 141-141    nd    nd
glc-2 3 261 147-393 2 439 135-744 2 475 207-744 2 387 171-603 2 336 333-339
glc-3 3 112 111-114 7 169 93-330 7 120 90-168 5 145 117-213 6 153 111-189
glc-4 2 702 249-1155 2 702 249-1155 2 702 249-1155 2 702 249-1155 1 972 972
  39-mer HSPs 41-mer HSPs 43-mer HSPs 45-mer HSPs 47-mer HSPs
ID # X ¯ R # X ¯ R # X ¯ R # X ¯ R # X ¯ R
lev-1 3 564 339-807 1 1392 1392 1 1401 1401 2 619 345-894 3 245 219-270
lev-8    nd    nd    nd    nd    nd
unc-29    nd    nd    nd    nd    nd
unc-38 1 1473 1473 1 1473 1473 2 868 264-1473 1 1473 1473    nd
unc-63    nd    nd    nd    nd    nd
avr-14 1 390 390 1 219 219    nd    nd    nd
avr-15 2 111 111-111     1 120 120 1 174 174 1 174 174
ben-1 7 100 75-120 10 138 90-234 16 115 84-234 25 114 87-348 15 160 90-453
glc-1    nd    nd    nd    nd    nd
glc-2    nd    nd    nd    nd    nd
glc-3 3 618 84-1383    nd 1 378 378    nd    nd
glc-4 1 1428 1428 1 1428 1428 1 972 972 1 972 972 1 1428 1428
  1. C. elegans target genes (name (ID), GenBank accession number (Acc #) and coding sequence length (CDS len)) used to BLASTx-query a database comprised of the initial de novo library assembly. For each k-mer (e.g. “21 mer HSPs”) are listed in columns the number of high scoring pairs identified (HSP; “#”), the mean HSP length in DNA bases (“ X ¯ ”), and the range of HSP-lengths (“R”) with minimum and maximum length shown. Bold HSP-length values indicates the longest HSP identified among all k-mers for a given target gene. “nd” indicate no high-similarity HSPs were identified at that k-mer.