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PMID: 15640440 Published · epublish English Journal Article Research Support, Non-U.S. Gov't Validation Study

ArrayOme: a program for estimating the sizes of microarray-visualized bacterial genomes.

Nucleic acids research ·Vol. 33 ·No. 1 ·2005-01-07 ·Pages e3

Ou HY, Smith R, Lucchini S, Hinton J, Chaudhuri RR, Pallen M, Barer MR, Rajakumar K

Abstract

ArrayOme is a new program that calculates the size of genomes represented by microarray-based probes and facilitates recognition of key bacterial strains carrying large numbers of novel genes. Protein-coding sequences (CDS) that are contiguous on annotated reference templates and classified as 'Present' in the test strain by hybridization to microarrays are merged into ICs (ICs). These ICs are then extended to account for flanking intergenic sequences. Finally, the lengths of all extended ICs are summated to yield the 'microarray-visualized genome (MVG)' size. We tested and validated ArrayOme using both experimental and in silico-generated genomic hybridization data. MVG sizing of five sequenced Escherichia coli and Shigella strains resulted in an accuracy of 97-99%, as compared to true genome sizes, when the comprehensive ShE.coli meta-array gene sequences (6239 CDS) were used for in silico hybridization analysis. However, the E.coli CFT073 genome size was underestimated by 14% as this meta-array lacked probes for many CFT073 CDS. ArrayOme permits rapid recognition of discordances between PFGE-measured genome and MVG sizes, thereby enabling high-throughput identification of strains rich in novel genes. Gene discovery studies focused on these strains will greatly facilitate characterization of the global gene pool accessible to individual bacterial species.

MeSH Terms
Computational Biology Escherichia coli K12/genetics Genome, Bacterial Genomics/methods Oligonucleotide Array Sequence Analysis/methods Shigella/genetics Software
Authors & Affiliations
8 authors, click to expand affiliations / ORCID
Ou Hong-Yu
Department of Infection, Immunity and Inflammation, Leicester Medical School, University of Leicester Leicester LE1 9HN, UK.
Smith Rebecca
Lucchini Sacha
Hinton Jay
Chaudhuri Roy R
Pallen Mark
Barer Michael R
Rajakumar Kumar
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Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gni005
Published
2005-01-07
Epub
2005-00-07
Pages
e3
Language
English
Region
England
NLM ID
0411011
PMCID
PMC546176
Subset
IM
External Links
PubMed source DOI: 10.1093/nar/gni005 PMC Full Text View journal details
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