Background: Gene family identification from ESTs can be a valuable resource for analysis of genome evolution but presents unique challenges in organisms for which the entire genome is not yet sequenced. We have developed a novel gene family identification method based on negative selection patterns (NSP) between family members to screen EST-generated contigs. This strategy was tested on five known gene families in Arabidopsis to see if individual paralogs could be identified with accuracy from EST data alone when compared to the actual gene sequences in this fully sequenced genome. Results: The NSP method uniquely identified family members in all the gene families tested. Two members of the FtsH gene family, three members each of the PAL, RF1, and ribosomal L6 gene families, and four members of the CAD gene family were correctly identified. Additionally all ESTs from the representative contigs when checked against MapViewer data successfully identify the gene locus predicted. Conclusion: We demonstrate the effectiveness of the NSP strategy in identifying specific gene family members in Arabidopsis using only EST data and we describe how this strategy can be used to identify many gene families in agronomically important crop species where they are as yet undiscovered.

Meeting Name

5th Annual MCBIOS Conference. Systems Biology: Bridging the Omics (2008: Feb. 23-24, Oklahoma City, OK)


Biological Sciences

Second Department

Computer Science

Keywords and Phrases

Arabidopsis; Gene families; Gene sequences; Genome evolution; Identification method; Identification strategies; Negative selection; Novel genes

International Standard Serial Number (ISSN)


Document Type

Article - Conference proceedings

Document Version

Final Version

File Type





© 2008 Frank et al., All rights reserved.

Publication Date

01 Jan 2008

PubMed ID