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xBASE2: a comprehensive resource for comparative bacterial genomics.

Chaudhuri RR, Loman NJ, Snyder LA, Bailey CM, Stekel DJ, Pallen MJ - Nucleic Acids Res. (2007)

Bottom Line: xBASE is a genome database aimed at helping laboratory-based bacteriologists make best use of bacterial genome sequence data, with a particular emphasis on comparative genomics.The latest version, xBASE 2.0 (http://xbase.bham.ac.uk), now provides comprehensive coverage of all bacterial genomes and features an updated modularized backend and an improved user interface, which includes a taxonomy browser and a powerful full-text search facility.

View Article: PubMed Central - PubMed

Affiliation: Centre for Systems Biology, University of Birmingham, Birmingham B15 2TT, UK.

ABSTRACT
xBASE is a genome database aimed at helping laboratory-based bacteriologists make best use of bacterial genome sequence data, with a particular emphasis on comparative genomics. The latest version, xBASE 2.0 (http://xbase.bham.ac.uk), now provides comprehensive coverage of all bacterial genomes and features an updated modularized backend and an improved user interface, which includes a taxonomy browser and a powerful full-text search facility.

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Related in: MedlinePlus

Alignment of two Staphylococcus aureus genomes, zoomed in to show the nucleotide sequence. The MW2 gene MW1571, which encodes a tRNA methyltransferase, is split into two in the NCTC 8325 genome. The display indicates that this is due to a single base deletion that occurs in a run of 5 T residues, suggesting that it may be an artefact caused by a sequencing error.
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Figure 3: Alignment of two Staphylococcus aureus genomes, zoomed in to show the nucleotide sequence. The MW2 gene MW1571, which encodes a tRNA methyltransferase, is split into two in the NCTC 8325 genome. The display indicates that this is due to a single base deletion that occurs in a run of 5 T residues, suggesting that it may be an artefact caused by a sequencing error.

Mentions: An XY plot allows the plotting of data such as nucleotide composition and principal axes derived from correspondence analysis of relative synonymous codon usage data (Figure 2). This facilitates identification of genes that show unusual patterns of composition or codon usage that might be indicative of horizontal gene transfer. The graphical display of genomic regions now includes genomic coordinates and at high zoom nucleotide sequences are displayed (Figure 3). Circular chromosomes and plasmids are now handled correctly, so the display can wrap around the origin of the sequence. An xBASE blog has been launched, with regular contributions from the development team, including status updates, discussions of new features and requests from users for additional functionality.Figure 2.


xBASE2: a comprehensive resource for comparative bacterial genomics.

Chaudhuri RR, Loman NJ, Snyder LA, Bailey CM, Stekel DJ, Pallen MJ - Nucleic Acids Res. (2007)

Alignment of two Staphylococcus aureus genomes, zoomed in to show the nucleotide sequence. The MW2 gene MW1571, which encodes a tRNA methyltransferase, is split into two in the NCTC 8325 genome. The display indicates that this is due to a single base deletion that occurs in a run of 5 T residues, suggesting that it may be an artefact caused by a sequencing error.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238843&req=5

Figure 3: Alignment of two Staphylococcus aureus genomes, zoomed in to show the nucleotide sequence. The MW2 gene MW1571, which encodes a tRNA methyltransferase, is split into two in the NCTC 8325 genome. The display indicates that this is due to a single base deletion that occurs in a run of 5 T residues, suggesting that it may be an artefact caused by a sequencing error.
Mentions: An XY plot allows the plotting of data such as nucleotide composition and principal axes derived from correspondence analysis of relative synonymous codon usage data (Figure 2). This facilitates identification of genes that show unusual patterns of composition or codon usage that might be indicative of horizontal gene transfer. The graphical display of genomic regions now includes genomic coordinates and at high zoom nucleotide sequences are displayed (Figure 3). Circular chromosomes and plasmids are now handled correctly, so the display can wrap around the origin of the sequence. An xBASE blog has been launched, with regular contributions from the development team, including status updates, discussions of new features and requests from users for additional functionality.Figure 2.

Bottom Line: xBASE is a genome database aimed at helping laboratory-based bacteriologists make best use of bacterial genome sequence data, with a particular emphasis on comparative genomics.The latest version, xBASE 2.0 (http://xbase.bham.ac.uk), now provides comprehensive coverage of all bacterial genomes and features an updated modularized backend and an improved user interface, which includes a taxonomy browser and a powerful full-text search facility.

View Article: PubMed Central - PubMed

Affiliation: Centre for Systems Biology, University of Birmingham, Birmingham B15 2TT, UK.

ABSTRACT
xBASE is a genome database aimed at helping laboratory-based bacteriologists make best use of bacterial genome sequence data, with a particular emphasis on comparative genomics. The latest version, xBASE 2.0 (http://xbase.bham.ac.uk), now provides comprehensive coverage of all bacterial genomes and features an updated modularized backend and an improved user interface, which includes a taxonomy browser and a powerful full-text search facility.

Show MeSH
Related in: MedlinePlus