Computational tools and Interoperability in Comparative ... - CBS

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Tools
information, as genetic diversity within a bacterial species can be enormous. When multiple
genomes are available for a species we can define its core genome (all genes that are present in
all genomes of that species), its pan-genome (all genes that have been found in that species)
and its dispensable genes that are responsible for the variation between isolates. Multiple
genomes per species, together with more metagenomic data and more archaeal genome
sequences, comprise our most urgent data gaps. The research tools for analysis of the
genomes are available. Generate the sequences and the feast can begin.
References
for Comparison of Bacterial Genomes
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ
(1990) Basic local alignment search tool. J Mol Biol
215: 403–410.
Binnewies TT, Hallin PF, Staerfeldt HH, Ussery DW
(2005) Genome update: proteome comparisons.
Microbiology 151: 1–4.
Binnewies TT, et al. (2006) Ten years of bacterial genome
sequencing: comparative-genomics-based discoveries.
Funct Integr Genomics 6: 165–185.
Carver TJ, Rutherford KM, Berriman M, Rajandream
MA, Barrell BG, Parkhill J (2005) ACT: the Artemis
Comparison Tool. Bioinformatics 21: 3422–3423.
Chang CH, Chang YC, Underwood A, Chiou CS, Kao CY
(2007) VNTRDB: a bacterial variable number tandem
repeat locus database. Nucleic Acids Res 35:
D416–D421.
Chen S, Lesnik EA, Hall TA, Sampath R, Griffey RH,
Ecker DJ, Blyn LB (2002) A bioinformatics based
approach to discover small RNA genes in the Escherichia
coli genome. Biosystems 65: 157–177.
Deloger M, El Karoui M, Petit MA (2009) A genomic
distance based on MUM indicates discontinuity between
most bacterial species and genera. J Bacteriol
191: 91–99.
Denoeud F, Vergnaud G (2004) Identification of polymorphic
tandem repeats by direct comparison of
genome sequence from different bacterial strains: a
web-based resource. BMC Bioinformatics 5: 4.
Field D, et al. (2008) The minimum information about a
genome sequence (MIGS) specification. Nature Biotechnol
26:541–547.
Foerstner KU, von Mering C, Hooper SD, Bork P (2005)
Environments shape the nucleotide composition of
genomes. EMBO Rep 6: 1208–1213.
Galagan JE, et al. (2002) The genome of M. acetivorans
reveals extensive metabolic and physiological diversity.
Genome Res 12: 532–542.
Giovannoni SJ, et al. (2005) Genome streamlining in a
cosmopolitan oceanic bacterium. Science 309:
1242–1245.
Gottesman S (2005) Micros for microbes: non-coding
regulatory RNAs in bacteria. Trends Genet 21:
399–404.
Griffiths-Jones S, Moxon S, Marshall M, Khanna A,
Eddy SR, Bateman A (2005) Rfam: annotating
non-coding RNAs in complete genomes. Nucleic
Acids Res 33: D121–D124.
Hallin PF, Binnewies TT, Ussery DW (2008) The genome
BLAST atlas - a GeneWiz extension for visualization
of whole-genome homology. Mol Biosyst 4: 363–371.
Hallin PF, Ussery DW (2004) CBS Genome Atlas
Database: a dynamic storage for bioinformatic results
and sequence data. Bioinformatics 20: 3682–3686.
Henz SR, Huson DH, Auch AF, Nieselt-Struwe K,
Schuster SC (2005) Whole-genome prokaryotic
phylogeny. Bioinformatics 21: 2329–2335.
Jensen LJ, Friis C, Ussery DW (1999) Three views of
microbial genomes. Res Microbiol 150: 773–777.
Kurtz S, Philippy A, Delcher AL, Smoot M, Shumway M,
Antonescu C, Salzberg SL (2004) Versatile and open
software for comparing large genomes. Genome Biol
5: R12.
Lagesen K, Hallin P, Rodland EA, Staerfeldt HH,
Rognes T, Ussery DW (2007) RNAmmer: consistent
and rapid annotation of ribosomal RNA genes.
Nucleic Acids Res 35: 3100–3108.
Lessner DJ, et al. (2006) An unconventional pathway for
reduction of CO 2 to methane in CO-grown Methanosarcina
acetivorans revealed by proteomics. Proc
Natl Acad Sci USA 103: 17921–17926.
Mussmann M, Richter M, Lombardot T, Meyerdierks A,
Kuever J, Kube M, Glöckner FO, Amann R (2005)
Clustered genes related to sulfate respiration in uncultured
prokaryotes support the theory of their
concomitant horizontal transfer. J Bacteriol. 187:
7126–7137.
Musto H, Naya H, Zavala A, Romero H, Alvarez-Valin F,
Bernardi G (2006) Genomic GC level, optimal
growth temperature, and genome size in prokaryotes.
Biochem Biophys Res Commun 347: 1–3.
Pedersen AG, Jensen LJ, Brunak S, Staerfeldt HH,
Ussery DW (2000) A DNA structural atlas for
Escherichia coli. J Mol Biol 299: 907–930.
Richter M, Kube M, Bazylinski DA, Lombardot T,
Glöckner FO, Reinhardt R, Schüler D (2007) Comparative
genome analysis of four magnetotactic