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Title: ArrayOme: a program for estimating the sizes of microarray-visualized bacterial genomes
Authors: Ou, Hong-Yu
Smith, Rebecca J.
Lucchini, Sacha
Hinton, Jay
Chaudhuri, Roy R.
Pallen, Mark
Barer, Michael R.
Rajakumar, Kumar
First Published: 2005
Publisher: Oxford University Press (OUP)
Citation: Nucleic Acids Research, 2005, 33, (1), p. e3
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 silicogenerated 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 highthroughput 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.
DOI Link: 10.1093/nar/gni005
ISSN: 0305-1048
eISSN: 1362-4962
Version: Publisher version
Status: Peer reviewed
Type: Article
Rights: Copyright © 2005, the authors, Nucleic Acids Research, Vol. 33 No. 1 © Oxford University Press 2005. The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use permissions, please contact The online version is also available from
Appears in Collections:Published Articles, Dept. of Infection, Immunity and Inflammation

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