News about the HGT-DB

News and previous releases:

February 2004 The genomes from Bacteroides thetaiotaomicron VPI-5482, Vibrio vulnificus CMCP6 chr. I, Vibrio vulnificus CMCP6 chr. II, Vibrio vulnificus YJ016 chr. I and Vibrio vulnificus YJ016 chr. II have been added.

12th July 2002 8 complete genomes have been added to the database. The genomes added are: Buchnera aphidicola Sg, Chlorobium tepidum, Methanosarcina mazei, Staphylococcus aureus MW2, Streptomyces coelicor, Xanthomonas campestris ATCC33913, Xanthomonas citris

28th of May 2002 Major modificacions have been added to the database:

Ribosomal proteins have been filtered in the horizontal gene transfer prediction. Now, annotated ribosomal proteins are not predicted as being acquired or not acquired. In the future, other highly expressed genes will also be filtered.
Correspondence analyses of relative synonymous codon usage have been reanalyzed. These analyses generate now a new page for each genome and correlations between the two major axes and some variables have been added.
The number of sequences analyzed and the mean values of Relative Synonymous Codon Usage (RSCU) values have been added in the main page of each genome.
12 complete genomes have been added to the database. The genomes added are: Agrobacterium tumefaciens str. C58 (U. Wash.) circular and linear chromosomes, Brucella melitensis chromosomes I and II, Clostridium perfringens, Corynebacterium glutamicum, Fusobacterium nucleatum, Methanopyrus kandleri, Methanosarcina acetivorans, Nostoc sp. PCC7120, Pyrobaculum aerophilum, Pyrococcus furiosus, Ralstonia solanacearum and Streptococcus pyogenes MGAS8232.
The second chromosome from Deinococcus radiodurans and Vibrio cholerae, and the linear chromosome from Agrobacterium tumefaciens str. C58 have also been added.
All the others genomes have been reanalyzed with the latest versions (March 2002) downloaded from the NCBI ftp server. Some of these versions differ significantly from previous ones.

21th of March 2002 The format of all the tables that contain the proposed horizontally transferred genes are now uniform. A link to the COG family (if any) has been added.

6th of November 2001 39 complete genomes have been added to the database. There are now 63 complete genomes. The organisms added are: Agrobacterium tumefaciens C58, Bacillus halodurans C-125, Buchnera sp APS, Campylobacter jejuni, Caulobacter crescentus, Chlamydophila muridarum, Chlamydophila pneumoniae AR39, Chlamydophila pneumoniae J138, Clostridium acetobutylicum ATCC824, Escherichia coli O157:H7, Escherichia coli O157:H7: EDL933, Halobacterium sp NRC-1, Lactobacillus lactis subsp. lactis IL1403 , Listeria innocua, Listeria monocytogenes EGD-e, Mesorhizobium loti, Mycobacterium leprae TN, Mycobacterium tuberculosis CDC1551, Mycoplasma pulmonis UAB CTIP, Neisseria meningitidis MC58, Neisseria meningitidis Z2491, Pasteurella multocida PM70, Pseudomonas aeruginosa PA01, Rickettsia conorii Malish 7, Salmonella enteria serovar Typhi CT18, Salmonella enterica serovar Typhimurium LT2, Sinorhizobium meliloti 1021, Staphylococcus aureus Mu50, Staphylococcus aureus N315, Streptococcus pneumoniae R6, Streptococcus pneumoniae TIGR4, Streptococcus pyogenes SF370, Sulfolobus solfataricus, Sulfolobus tokodaii, Thermoplasma acidophilum, Thermoplasma volcanium, Vibrio cholerae, Xylella fastidiosa, Yersinia pestis CO92

November 2000 The HGT-DB has been created. It contains 24 archaeal and bacterial complete genomes: Aeropyrum pernix, Aquifex aeolicus, Archaeoglobus fulgidus, Bacillus subtilis, Borrelia burgdorferi, Chlamydia trachomatis, Chlamydia pneumoniae CWL209, Deinococcus radiodurans, Escherichia coli K-12, Haemophilus influenzae, Helicobacter pylori 26695, Helicobacter pylori J99, Methanococcus jannaschii, Methanobacterium thermoautotrophicum, Mycobacterium tuberculosis H37Rv, Mycoplasma genitalium, Mycoplasma pneumoniae, Pyrococcus abyssi,Pyrococcus horikoshii, Rickettsia prowazekii, Synechocystis PCC6803, Thermotoga maritima, Treponema pallidum, Ureaplasma urealyticum

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February 2004	The genomes from Bacteroides thetaiotaomicron VPI-5482, Vibrio vulnificus CMCP6 chr. I, Vibrio vulnificus CMCP6 chr. II, Vibrio vulnificus YJ016 chr. I and Vibrio vulnificus YJ016 chr. II have been added.
12th July 2002	8 complete genomes have been added to the database. The genomes added are: Buchnera aphidicola Sg, Chlorobium tepidum, Methanosarcina mazei, Staphylococcus aureus MW2, Streptomyces coelicor, Xanthomonas campestris ATCC33913, Xanthomonas citris
28th of May 2002	Major modificacions have been added to the database: Ribosomal proteins have been filtered in the horizontal gene transfer prediction. Now, annotated ribosomal proteins are not predicted as being acquired or not acquired. In the future, other highly expressed genes will also be filtered. Correspondence analyses of relative synonymous codon usage have been reanalyzed. These analyses generate now a new page for each genome and correlations between the two major axes and some variables have been added. The number of sequences analyzed and the mean values of Relative Synonymous Codon Usage (RSCU) values have been added in the main page of each genome. 12 complete genomes have been added to the database. The genomes added are: Agrobacterium tumefaciens str. C58 (U. Wash.) circular and linear chromosomes, Brucella melitensis chromosomes I and II, Clostridium perfringens, Corynebacterium glutamicum, Fusobacterium nucleatum, Methanopyrus kandleri, Methanosarcina acetivorans, Nostoc sp. PCC7120, Pyrobaculum aerophilum, Pyrococcus furiosus, Ralstonia solanacearum and Streptococcus pyogenes MGAS8232. The second chromosome from Deinococcus radiodurans and Vibrio cholerae, and the linear chromosome from Agrobacterium tumefaciens str. C58 have also been added. All the others genomes have been reanalyzed with the latest versions (March 2002) downloaded from the NCBI ftp server. Some of these versions differ significantly from previous ones.
21th of March 2002	The format of all the tables that contain the proposed horizontally transferred genes are now uniform. A link to the COG family (if any) has been added.
6th of November 2001	39 complete genomes have been added to the database. There are now 63 complete genomes. The organisms added are: Agrobacterium tumefaciens C58, Bacillus halodurans C-125, Buchnera sp APS, Campylobacter jejuni, Caulobacter crescentus, Chlamydophila muridarum, Chlamydophila pneumoniae AR39, Chlamydophila pneumoniae J138, Clostridium acetobutylicum ATCC824, Escherichia coli O157:H7, Escherichia coli O157:H7: EDL933, Halobacterium sp NRC-1, Lactobacillus lactis subsp. lactis IL1403 , Listeria innocua, Listeria monocytogenes EGD-e, Mesorhizobium loti, Mycobacterium leprae TN, Mycobacterium tuberculosis CDC1551, Mycoplasma pulmonis UAB CTIP, Neisseria meningitidis MC58, Neisseria meningitidis Z2491, Pasteurella multocida PM70, Pseudomonas aeruginosa PA01, Rickettsia conorii Malish 7, Salmonella enteria serovar Typhi CT18, Salmonella enterica serovar Typhimurium LT2, Sinorhizobium meliloti 1021, Staphylococcus aureus Mu50, Staphylococcus aureus N315, Streptococcus pneumoniae R6, Streptococcus pneumoniae TIGR4, Streptococcus pyogenes SF370, Sulfolobus solfataricus, Sulfolobus tokodaii, Thermoplasma acidophilum, Thermoplasma volcanium, Vibrio cholerae, Xylella fastidiosa, Yersinia pestis CO92
November 2000	The HGT-DB has been created. It contains 24 archaeal and bacterial complete genomes: Aeropyrum pernix, Aquifex aeolicus, Archaeoglobus fulgidus, Bacillus subtilis, Borrelia burgdorferi, Chlamydia trachomatis, Chlamydia pneumoniae CWL209, Deinococcus radiodurans, Escherichia coli K-12, Haemophilus influenzae, Helicobacter pylori 26695, Helicobacter pylori J99, Methanococcus jannaschii, Methanobacterium thermoautotrophicum, Mycobacterium tuberculosis H37Rv, Mycoplasma genitalium, Mycoplasma pneumoniae, Pyrococcus abyssi,Pyrococcus horikoshii, Rickettsia prowazekii, Synechocystis PCC6803, Thermotoga maritima, Treponema pallidum, Ureaplasma urealyticum