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| Title: | An automated method for rapid identification of putative gene family members in plants | |
| Author (s): | Frank, Ronald L. Mane, Ajay Ercal, Fikret | |
| Department/Lab Affiliations: | Biological Sciences Computer Science | |
| Keywords: | Arabidopsis Gene duplication Glycine max Putative Gene | |
| Issue Date: | 2006-09-26 | |
| Publisher: | BioMed Central | |
| Citation: | Frank, Ronald L., Mane, Ajay., and Ercal, Fikret. "An Automated Method for Rapid Identification of Putative Gene Family Members in Plants." BMC Bioinformatics, (2006). | |
| Abstract: | Gene 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. RESULTS : In 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. CONCLUSION : Gene 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. | |
| Type: | Article - Journal text | |
| In Title: | BMC Bioinformatics | |
| Copyright Notice: | This material is presented to ensure timely dissemination of scholarly and technical work. Copyright and all rights therein are retained by authors or by other copyright holders. All persons copying this information are expected to adhere to the terms and constraints invoked by each author's copyright. In most cases, these works may not be reposted without the explicit permission of the copyright holder. FULL COPYRIGHT INFORMATION: | |
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| title | An automated method for rapid identification of putative gene family members in plants | |
| contributor.author | Frank, Ronald L. | |
| contributor.author | Mane, Ajay | |
| contributor.author | Ercal, Fikret | |
| contributor.deptlab | Biological Sciences | |
| contributor.deptlab | Computer Science | |
| subject | Arabidopsis | |
| subject | Gene duplication | |
| subject | Glycine max | |
| subject | Putative Gene | |
| date.issued | 2006-09-26 | |
| publisher | BioMed Central | |
| identifier.citation | Frank, Ronald L., Mane, Ajay., and Ercal, Fikret. "An Automated Method for Rapid Identification of Putative Gene Family Members in Plants." BMC Bioinformatics, (2006). | |
| identifier.pub.URI | ||
| description.abstract | Gene 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. RESULTS : In 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. CONCLUSION : Gene 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. | |
| type | Article - Journal | |
| type.DCMIType | text | |
| type.status | Final version | |
| rights | This material is presented to ensure timely dissemination of scholarly and technical work. Copyright and all rights therein are retained by authors or by other copyright holders. All persons copying this information are expected to adhere to the terms and constraints invoked by each author's copyright. In most cases, these works may not be reposted without the explicit permission of the copyright holder. | |
| rights.URI | ||
| relation.isPartOf | BMC Bioinformatics | |
| date.accessioned | 2008-04-09T18:41:18Z | |
| date.available | 2008-04-09T18:41:17Z | |
| identifier.persist.URI | ||
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