ArticleNucleic acids research2005
ArrayOme: a program for estimating the sizes of microarray-visualized bacterial genomes.
Article in Nucleic acids research, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- mGenomeSubtractor: a web-based tool for parallel in silico subtractive hybridization analysis of multiple bacterial genomes.Nucleic acids research · 2010Article
- Translational genomics to develop a Salmonella enterica serovar Paratyphi A multiplex polymerase chain reaction assay.The Journal of molecular diagnostics : JMD · 2007Article
- MobilomeFINDER: web-based tools for in silico and experimental discovery of bacterial genomic islands.Nucleic acids research · 2007Article
- Survey of genomic diversity among Enterococcus faecalis strains by microarray-based comparative genomic hybridization.Applied and environmental microbiology · 2007Article
- Prediction of effective genome size in metagenomic samples.Genome biology · 2007Article
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8 authors.
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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.
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