ArticleBMC bioinformatics2006
An automated method for rapid identification of putative gene family members in plants.
Article in BMC bioinformatics, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed, 12 citations in OpenAlex.
- TARGeT: a web-based pipeline for retrieving and characterizing gene and transposable element families from genomic sequences.Nucleic acids research · 2009Article
- Validation of an NSP-based (negative selection pattern) gene family identification strategy.BMC bioinformatics · 2008Article
- Proceedings of the Fourth Annual Conference of the MidSouth Computational Biology and Bioinformatics Society.BMC bioinformatics · 2007Article
- Proceedings of the Third Annual Conference of the MidSouth Computational Biology and Bioinformatics Society. Introduction.BMC bioinformatics · 2006Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundGene duplication events have played a significant role in genome evolution, particularly in plants. Exhaustive searches for all members of a known gene family as well as the identification of new gene families has become increasingly important. Subfunctionalization via changes in regulatory sequences following duplication (adaptive selection) appears to be a common mechanism of evolution in plants and can be accompanied by purifying selection on the coding region. Such negative selection can be detected by a bias toward synonymous over nonsynonymous substitutions. However, the process of identifying this bias requires many steps usually employing several different software programs. We have simplified the process and significantly shortened the time required by condensing many steps into a few scripts or programs to rapidly identify putative gene family members beginning with a single query sequence.
resultsIn this report we 1) describe the software tools (SimESTs, PCAT, and SCAT) developed to automate the gene family identification, 2) demonstrate the validity of the method by correctly identifying 3 of 4 PAL gene family members from Arabidopsis using EST data alone, 3) identify 2 to 6 CAD gene family members from Glycine max (previously unidentified), and 4) identify 2 members of a putative Glycine max gene family previously unidentified in any plant species.
conclusionGene families in plants, particularly that subset where purifying selection has occurred in the coding region, can be identified quickly and easily by integrating our software tools and commonly available contig assembly and ORF identification programs.
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