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May 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  
-------------------------------------------------------------
*  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 Total bank  22257  rejected =  1090  extracted  21167

Bacteria house keeping genes

* sod          bank  1316  rejected =  16  extracted  1300 
* groel2-hsp65 bank   759  rejected =  15  extracted  744
* tuf          bank   653  rejected =  4  extracted  649
* rpoB         bank  4744  rejected =  404  extracted  4340
* recA         bank  3628  rejected =  102  extracted  3526
* tmRNA        bank   534  rejected =  22  extracted  512
* glyA         bank   329  rejected =  9  extracted  320
* groes        bank  555  rejected =  115  extracted  440
* groel-hsp60-65  bank  5211  rejected =  376  extracted  4835
* gyrB         bank  5255  rejected =  111  extracted  5144
* fusA         bank  423  rejected =  7  extracted  416

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 gyrB NB: This database was accidentally missing since last month
Bacteria_gyrB_lax Nb Seqs  0 -> 5144  added= 5144
Bacteria_gyrB_lax TS  0 -> 892  C analysis  0 -> 217 Nb T/C old  0  new  1109 TSC added=  1109

*   Bacteria_dnaJ_lax (new)
Bacteria_dnaJ_lax Nb Seqs  0 -> 505  added= 505
Bacteria_dnaJ_lax TS  0 -> 140  C analysis  0 -> 236 Nb T/C old  0  new  376 TSC added=  376
*   Bacteria_dnaK_lax (new)
Bacteria_dnaK_lax Nb Seqs  0 -> 692  added= 692
Bacteria_dnaK_lax TS  0 -> 159  C analysis  0 -> 236 Nb T/C old  0  new  395 TSC added=  395
*   Bacteria_fusA_lax (new)
Bacteria_fusA_lax Nb Seqs  0 -> 416  added= 416
Bacteria_fusA_lax TS  0 -> 57  C analysis  0 -> 182 Nb T/C old  0  new  239 TSC added=  239
*   Bacteria_tuf_lax
Bacteria_tuf_lax Nb Seqs  636 -> 649  added= 13
Bacteria_tuf_lax TS  260 -> 271  C analysis  91 -> 92 Nb T/C old  351  new  363 TSC added=  12
*   Bacteria_sodA_lax
Bacteria_sodA_lax Nb Seqs  1237 -> 1300  added= 63
Bacteria_sodA_lax TS  349 -> 355  C analysis  108 -> 110 Nb T/C old  457  new  465 TSC added=  8
*   Actinobacteria_groel2-hsp65_lax
Actinobacteria_groel2-hsp65_lax Nb Seqs  743 -> 744  added= 1
Actinobacteria_groel2-hsp65_lax TS  316 -> 316  C analysis  0 -> 0 Nb T/C old  316  new  316 TSC added=  0
*   Bacteria_rpob_lax
Bacteria_rpob_lax Nb Seqs  4327 -> 4340  added= 13
Bacteria_rpob_lax TS  1185 -> 1191  C analysis  212 -> 220 Nb T/C old  1397  new  1411 TSC added=  14
*   Bacteria_recA_lax
Bacteria_recA_lax Nb Seqs  3447 -> 3526  added= 79
Bacteria_recA_lax TS  720 -> 726  C analysis  218 -> 225 Nb T/C old  938  new  951 TSC added=  13
*   Bacteria_tmRNA_lax
Bacteria_tmRNA_lax Nb Seqs  499 -> 512  added= 13
Bacteria_tmRNA_lax TS  197 -> 199  C analysis  143 -> 156 Nb T/C old  340  new  355 TSC added=  15
*   Archaea_SSU-rDNA-16S_lax 
Archaea_SSU-rDNA-16S_lax Nb Seqs  20774 -> 21167  added= 393
Archaea_SSU-rDNA-16S_lax TS  378 -> 384  C analysis  35 -> 37 Nb T/C old  413  new  421 TSC added=  8
*   Bacteria_SSU-rDNA-16S_lax 
Bacteria_SSU-rDNA-16S_lax Nb Seqs  182881 -> 186738  added= 3857
Bacteria_SSU-rDNA-16S_lax TS  9622 -> 9710  C analysis  1323 -> 1410 Nb T/C old  10945  new  11120 TSC added=  175
*  Bacteria_glyA_lax (new)
ux_Bact_glyA_lax Nb Seqs  0 -> 320  added= 320
ux_Bact_glyA_lax TS  0 -> 48  C analysis  0 -> 211 Nb T/C old  0  new  259 TSC added=  259
* Bacteria_groES (new)
ux_groes-bacteria Nb Seqs  0 -> 440  added= 440
ux_groes-bacteria TS  0 -> 59  C analysis  0 -> 160 Nb T/C old  0  new  219 TSC added=  219
* Bacteria groEL1+2 Hsp60?+65 (new)
ux_Bacteria_groel-hsp60-65_lax Nb Seqs  0 -> 4835  added= 4835
ux_Bacteria_groel-hsp60-65_lax TS  0 -> 918  C analysis  0 -> 176 Nb T/C old  0  new  1094 TSC added=  1094

Sun Aug 17 11:33:56 2008

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