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Validation Of An Nsp-Based (Negative Selection Pattern) Gene Family Identification Strategy, Ronald L. Frank, Cyriac Kandoth, Fikret Erçal
Validation Of An Nsp-Based (Negative Selection Pattern) Gene Family Identification Strategy, Ronald L. Frank, Cyriac Kandoth, Fikret Erçal
Biological Sciences Faculty Research & Creative Works
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 …
An Automated Method For Rapid Identification Of Putative Gene Family Members In Plants, Ronald L. Frank, Ajay Mane, Fikret Erçal
An Automated Method For Rapid Identification Of Putative Gene Family Members In Plants, Ronald L. Frank, Ajay Mane, Fikret Erçal
Biological Sciences Faculty Research & Creative Works
Background: 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 …
Evaluation Of Glycine Max Mrna Clusters, Ronald L. Frank, Fikret Erçal
Evaluation Of Glycine Max Mrna Clusters, Ronald L. Frank, Fikret Erçal
Biological Sciences Faculty Research & Creative Works
Background: Clustering the ESTs from a large dataset representing a single species is a convenient starting point for a number of investigations into gene discovery, genome evolution, expression patterns, and alternatively spliced transcripts. Several methods have been developed to accomplish this, the most widely available being UniGene, a public domain collection of gene-oriented clusters for over 45 different species created and maintained by NCBI. The goal is for each cluster to represent a unique gene, but currently it is not known how closely the overall results represent that reality. UniGene's build procedure begins with initial mRNA clusters before joining ESTs. …