Extraction April 07
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April 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.bnk 25279 23594 rejected= 1685
* DeinococcusThermus?.bnk 531 503 rejected= 28
* Aquificae.bnk 952 941 rejected= 11
* Bacteroidetes_Chlorobi.bnk 14263 13539 rejected= 724
* Chlamydiae_Verrucomicrobia.bnk 1794 1568 rejected= 226
* Chloroflexi.bnk 2028 1979 rejected= 49
* Chrysiogenetes.bnk 1 1 rejected= 0
* Cyanobacteria.bnk 8381 7777 rejected= 604
* Deferribacteres.bnk 94 92 rejected= 2
* Dictyoglomi.bnk 10 10 rejected= 0
* Fibrobacteres_Acidobacteria.bnk 3905 3867 rejected= 38
* Firmicutes.bnk 33246 30557 rejected= 2689
* Fusobacteria.bnk 603 521 rejected= 82
* Gemmatimonadetes.bnk 403 399 rejected= 4
* Nitrospirae.bnk 471 450 rejected= 21
* Planctomycetes.bnk 2702 2662 rejected= 40
* Proteobacteria.bnk 89664 83207 rejected= 6457
* Spirochaetes.bnk 2809 2617 rejected= 192
* Thermodesulfobacteria.bnk 104 102 rejected= 2
* Thermotogae.bnk 129 118 rejected= 11
* Unclassified.bnk 8723 8377 rejected= 346
* Total Bacteria SSUrDNA 196092 182881
SSU rDNA Archaea
* Archaea Total bank : 21804 Total rejected : 1030 Total extracted : 20774
Bacteria house keeping genes
* gyrB Total bank : 4863 Total rejected : 111 Total extracted : 4752 * sod Total bank : 1253 Total rejected : 16 Total extracted : 1237 * groel2-hsp65 Total bank : 758 Total rejected : 15 Total extracted : 743 * tuf Total bank : 640 Total rejected : 4 Total extracted : 636 * rpoB Total bank : 4731 Total rejected : 404 Total extracted : 4327 * recA Total bank : 3549 Total rejected : 102 Total extracted : 3447 * tmRNA Total bank : 521 Total rejected : 22 Total extracted : 499
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
* Bacteria_tuf_lax Bacteria_tuf_lax Nb Seqs 634 -> 636 added= 2 Bacteria_tuf_lax TS 259 -> 260 C analysis 90 -> 91 Nb T/C old 349 new 351 TSC added= 2 * Bacteria_sodA_lax Bacteria_sodA_lax Nb Seqs 1234 -> 1237 added= 3 Bacteria_sodA_lax TS 349 -> 349 C analysis 106 -> 108 Nb T/C old 455 new 457 TSC added= 2 * Actinobacteria_groel2-hsp65_lax Actinobacteria_groel2-hsp65_lax Nb Seqs 743 -> 743 added= 0 Actinobacteria_groel2-hsp65_lax TS 315 -> 316 C analysis 0 -> 0 Nb T/C old 315 new 316 TSC added= 1 * Bacteria_rpob_lax Bacteria_rpob_lax Nb Seqs 4261 -> 4327 added= 66 Bacteria_rpob_lax TS 1175 -> 1185 C analysis 207 -> 212 Nb T/C old 1382 new 1397 TSC added= 15 * Bacteria_recA_lax Bacteria_recA_lax Nb Seqs 3437 -> 3447 added= 10 Bacteria_recA_lax TS 720 -> 720 C analysis 213 -> 218 Nb T/C old 933 new 938 TSC added= 5 * Bacteria_tmRNA_lax Bacteria_tmRNA_lax Nb Seqs 493 -> 499 added= 6 Bacteria_tmRNA_lax TS 197 -> 197 C analysis 138 -> 143 Nb T/C old 335 new 340 TSC added= 5 * Archaea_SSU-rDNA-16S_lax Archaea_SSU-rDNA-16S_lax Nb Seqs 19922 -> 20774 added= 852 Archaea_SSU-rDNA-16S_lax TS 376 -> 378 C analysis 32 -> 35 Nb T/C old 408 new 413 TSC added= 5 * Archaea_SSU-rDNA-16S_stringent Archaea_SSU-rDNA-16S_stringent Nb Seqs ? -> 413 added= ? Archaea_SSU-rDNA-16S_stringent TS 376 -> 378 C analysis 32 -> 35 Nb T/C old 408 new 413 TSC added= 5 * Bacteria_TS_SSU-rDNA-16S_stringent Bacteria_TS_SSU-rDNA-16S_stringent Nb Seqs 11133 -> 10796 added= 337 Bacteria_TS_SSU-rDNA-16S_stringent TS 9528 -> 9797 C analysis 1268 -> 1323 Nb T/C old 10796 new 11120 TSC added= 324 * Bacteria_SSU-rDNA-16S_lax Bacteria_SSU-rDNA-16S_lax Nb Seqs 182881 -> 177066 added= 5815 Bacteria_SSU-rDNA-16S_lax TS 9528 -> 9622 C analysis 1268 -> 1323 Nb T/C old 10796 new 10945 TSC added= 149
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