Extraction Jun 07
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June 07 Extractions
This table gives the number of sequences in the monthly extracted bank and the number of sequences in Bibi Data Bases. Note that shortest sequences are rejected (usually <300 nucleotides) as well as sequences >3000 for 16S SSU-rDNA.
SSU rDNA bacteria
Group Bank BIBI DB
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* Actinobacteria bank 25802 rejected = 1704 extracted 24098
* DeinococcusThermus? bank 534 rejected = 28 extracted 506
* Aquificae bank 954 rejected = 11 extracted 943
* Bacteroidetes_Chlorobi bank 14541 rejected = 777 extracted 13764
* Chlamydiae_Verrucomicrobia bank 1822 rejected = 227 extracted 1595
* Chloroflexi bank 2076 rejected = 51 extracted 2025
* Chrysiogenetes bank 1 rejected = 0 extracted 1
* Cyanobacteria bank 8839 rejected = 648 extracted 8191
* Deferribacteres bank 95 rejected = 2 extracted 93
* Dictyoglomi bank 10 rejected = 0 extracted 10
* Fibrobacteres_Acidobacteria bank 4007 rejected = 51 extracted 3956
* Firmicutes bank 34092 rejected = 2865 extracted 31227
* Fusobacteria bank 603 rejected = 82 extracted 521
* Gemmatimonadetes bank 410 rejected = 4 extracted 406
* Nitrospirae bank 473 rejected = 23 extracted 450
* Planctomycetes bank 2790 rejected = 45 extracted 2745
* Proteobacteria bank 91284 rejected = 6550 extracted 84734
* Spirochaetes bank 2820 rejected = 192 extracted 2628
* Thermodesulfobacteria bank 104 rejected = 2 extracted 102
* Thermotogae bank 129 rejected = 11 extracted 118
* Unclassified bank 8957 rejected = 332 extracted 8625
Total bank : 200343 Total rejected : 13605 Total extracted : 186738
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SSU rDNA Archaea
* Archaea bank 22603 rejected = 1093 extracted 21510
Bacteria house keeping genes
* sod bank : 1346 Total rejected : 16 extracted : 1330 * groEL2-hsp65 Actino : 810 Total rejected : 15 extracted : 795 * groEL2 Bacteria : 3298 rejected = 373 extracted 2925 * tuf bank 668 rejected = 4 extracted 664 * rpoB bank 5313 rejected = 753 extracted 4560 * recA bank 3952 rejected = 102 extracted 3850 * tmRNA bank 542 rejected = 22 extracted 520 * glyA bank 346 rejected = 9 extracted 337 * groes bank 563 rejected = 116 extracted 447 * gyrB bank : 5511 Total rejected : 134 extracted : 5377 * fusA bank 432 rejected = 7 extracted 425 * dnaJ bank 644 rejected = 45 extracted 599 * dnaK bank 1080 rejected = 153 extracted 927
TS extraction
TS= Type Strain C=Complete or partially complete genomes
How to read this table * Gene Gene Nb Seqs seq nb previous -> seq nb current added= nb added Gene TS previous nb TS -> current nb TS C analysis previous nb C -> current nb C Nb T/C old xx new xx TSC added= x
############### Verification previous vs actual ################## * ux_Bact_glyA_lax ux_Bact_glyA_lax: ux_Bact_glyA_lax Nb Seqs 0 -> 337 added= 337 ux_Bact_glyA_lax: ux_Bact_glyA_lax TS 0 -> 49 C analysis 0 -> 219 Nb T/C old 0 new 268 TSC added= 268 * ux_Bacteria_dnaJ_lax ux_Bacteria_dnaJ_lax Nb Seqs 505 -> 599 added= 94 ux_Bacteria_dnaJ_lax TS 140 -> 225 C analysis 236 -> 244 Nb T/C old 376 new 469 TSC added= 93 * ux_Bacteria_dnaK_lax ux_Bacteria_dnaK_lax Nb Seqs 692 -> 927 added= 235 ux_Bacteria_dnaK_lax TS 159 -> 163 C analysis 236 -> 247 Nb T/C old 395 new 410 TSC added= 15 * ux_Actinobacteria_groel2-hsp65_lax ux_Actinobacteria_groel2-hsp65_lax Nb Seqs 744 -> 795 added= 51 ux_Actinobacteria_groel2-hsp65_lax TS 316 -> 317 C analysis 0 -> 0 Nb T/C old 316 new 317 TSC added= 1 * ux_Bacteria_groEL_lax ux_Bacteria_groEL_lax: Aucun fichier ou répertoire de ce type ux_Bacteria_groEL_lax Nb Seqs 0 -> 2925 added= 2925 ux_Bacteria_groEL_lax TS 0 -> 581 C analysis 0 -> 152 Nb T/C old 0 new 733 TSC added= 733 * ux_Bacteria_groes-cpn10_lax ux_Bacteria_groes-cpn10_lax Nb Seqs 0 -> 447 added= 447 ux_Bacteria_groes-cpn10_lax TS 0 -> 59 C analysis 0 -> 167 Nb T/C old 0 new 226 TSC added= 226 * ux_Bacteria_fusA_lax ux_Bacteria_fusA_lax Nb Seqs 416 -> 425 added= 9 ux_Bacteria_fusA_lax TS 57 -> 60 C analysis 182 -> 189 Nb T/C old 239 new 249 TSC added= 10 * ux_Bacteria_tuf_lax ux_Bacteria_tuf_lax Nb Seqs 649 -> 664 added= 15 ux_Bacteria_tuf_lax TS 271 -> 272 C analysis 92 -> 97 Nb T/C old 363 new 369 TSC added= 6 * ux_Bacteria_sodA_lax ux_Bacteria_sodA_lax Nb Seqs 1300 -> 1330 added= 30 ux_Bacteria_sodA_lax TS 355 -> 355 C analysis 110 -> 112 Nb T/C old 465 new 467 TSC added= 2 * Bacteria_rpob_lax Bacteria_rpob_lax Nb Seqs 4340 -> 4560 added= 220 Bacteria_rpob_lax TS 1191 -> 1237 C analysis 220 -> 230 Nb T/C old 1411 new 1467 TSC added= 56 * Bacteria_recA_lax Bacteria_recA_lax Nb Seqs 3526 -> 3850 added= 324 Bacteria_recA_lax TS 726 -> 739 C analysis 225 -> 235 Nb T/C old 951 new 974 TSC added= 23 * ux_Bacteria_tmRNA_lax ux_Bacteria_tmRNA_lax Nb Seqs 512 -> 520 added= 8 ux_Bacteria_tmRNA_lax TS 199 -> 201 C analysis 156 -> 162 Nb T/C old 355 new 363 TSC added= 8 * Archaea_SSU-rDNA-16S_lax Archaea_SSU-rDNA-16S_lax Nb Seqs 21167 -> 21510 added= 343 Archaea_SSU-rDNA-16S_lax TS 384 -> 387 C analysis 37 -> 37 Nb T/C old 421 new 424 TSC added= 3 * Bacteria_SSU-rDNA-16S_lax Bacteria_SSU-rDNA-16S_lax Nb Seqs 186738 -> 190594 added= 3856 Bacteria_SSU-rDNA-16S_lax TS 9710 -> 9822 C analysis 1410 -> 1462 Nb T/C old 11120 new 11284 TSC added= 164 ############### total seq ################## 229483
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