Bioinformatics and Functional Genomics

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Chapter 14: Completed genomes: bacteria and archaea

Web resources from Chapter 14
Website URL
GSS database http://www.ncbi.nlm.nih.gov/dbGSS/index.html
HTGS homepage http://www.ncbi.nlm.nih.gov/HTGS/
The Protein Data Bank http://www.rcsb.org/pdb/
LocusLink http://www.ncbi.nlm.nih.gov/LocusLink/
Entrez http://www.ncbi.nlm.nih.gov/Entrez/
Entrez tutorials http://www.ncbi.nlm.nih.gov/Education/index.html
Ensembl http://www.ensembl.org
The Wellcome Trust Sanger Institute http://www.sanger.ac.uk/
EMBL http://www.ebi.ac.uk/embl/
EXPASY http://www.expasy.ch/
SRS portal of EXPASY http://www.expasy.ch/srs5/
LION Biosciences http://www.lionbioscience.com
Publicly available SRS servers http://downloads.lionbio.co.uk/publicsrs.html
PIR http://pir.georgetown.edu/
PubMed http://www.ncbi.nlm.nih.gov/PubMed/
SRS at The European Bioinformatics Instititute http://srs.ebi.ac.uk/
PubMed tutorial http://www.nlm.nih.gov/bsd/pubmed_tutorial/m1001.html
The growth of Medline http://www.nlm.nih.gov/bsd/medline_growth.html
Medline statistics for articles in the English language http://www.nlm.nih.gov/bsd/medline_lang_distr.html
ARL http://www.arl.org/scomm/edir/index.html
MESH website http://www.nlm.nih.gov/mesh/meshhome.html

 

Tables

Table 14-8. Programs for gene-finding in prokaryotic genomes.
Program Description
Glimmer At TIGR, this is one of the best programs
ECOPARSE ecoparse@cse.ucsc.edu
GeneMark.fbf  
GeneMark.hmm Uses hidden Markov models
GeneMarkS Improved accuracy of predicting gene start sites
Orpheus Gene prediction in complete bacterial genomes and large genomic fragments.
 
 
Table 14-8. Completed bacterial genomes. Abbreviations: Mbp, megabase pairs (millions of base pairs); ORFs, open reading frames.
Bacterium Accession
Aquifex aeolicus NC_000918
Bacillus halodurans NC_002570
Bacillus subtilis NC_000964
Borrelia burgdorferi NC_001318
Borrelia burgdorferi NC_001318
Buchnera sp. NC_002528
Campylobacter jejuni NC_002163
Caulobacter crescentus NC_002696
Chlamydia pneumoniae CWL029 NC_000922
Chlamydia pneumoniae AR39 NC_002179
Chlamydia pneumoniae J138 NC_002491
C. trachomatis serovar D (D/UW-3/Cx) NC_000117
C. trachomatis MoPn NC_002620
Deinococcus radiodurans NC_1263
Escherichia coli K-12 Strain NC_000913
Escherichia coli O157:H7 (RIMD 0509952) NC_002695
Escherichia coli O157:H7 strain NC_002655
Haemophilus influenzae NC_000907
Helicobacter pylori 26695 NC_000915
Helicobacter pylori J99 NC_000921
Lactococcus lactis sbsp lactis NC_002662
Mesorhizobium loti NC_002678
Mycobacterium leprae NC_002677
Mycobacterium tuberculosis H37Rv NC_000962
Mycoplasma genitalium NC_000908
Mycobacterium pneumoniae NC_000912
Mycoplasma pulmonis NC_002771
Neisseria meningitidis MC58 NC_002183
Neisseria meningitidis serogroup A strain Z2491 NC_002203
Pasteurella multocida NC_002663
Pseudomonas aeruginosa NC_002516
Rickettsia prowazekii NC_000963
Staphylococcus aureus NC_002745
Synechocystis sp. NC_000911
Thermotoga maritima NC_000853
Treponema pallidum NC_000919
Ureaplasma urealyticum NC_002162
Vibrio cholerae NC_002505
Vibrio cholerae NC_002506
Xylella fstidiosa NC_002488
 
Table 14-9. Completed archaeal genomes. Abbreviations: Mbp, megabase pairs (millions of base pairs); ORFs, open reading frames.
Archaeon Accession (GenBank)
Aeropyrum pernix NC_000854
Archaoglobus fulgidus NC_000917
Halobacterium sp NC_002607
Methanobacterium thermotautotrophicum NC_000916
Methanococcus jannaschii NC_000909
Pyrococcus horikoshii NC_000961
Thermoplasma acidophilum NC_002578
Thermoplasma volcanium NC_002689
 
Table 14-10. Internet resources for the study of bacterial genomes.
Resource Description
Prokaryotic Ongoing Genome Projects Prokaryotic Genome Projects
TIGR Microbial database
Washington University Bacterial genomes
University of Oklahoma  
The Sanger Center Microbial genomes
MBGD Microbial genome database
EcoCyc  
 
 
 
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