Panning for genes--A visual strategy for identifying novel gene orthologs and paralogs.

ABSTRACT: We have developed a rapid visual method for identifying novel members of gene families. Starting with an evolutionary tree, 20-50 protein query sequences for a gene family are selected from different branches of the tree. These query sequences are used to search the GenBank and expressed sequence tag (EST) DNA databases and their nightly updates using the tfastx3 or tfasty3 programs. The results of all 20-50 searches are collated and resorted to highlight EST or genomic sequences that share significant similarity with the query sequences. The statistical significance of each DNA/protein alignment is plotted, highlighting the portion of the query sequence that is present in the database sequence and the percent identity in the aligned region. The collated results for database sequences are

SUBMITTER: Retief JD 

PROVIDER: S-EPMC310732 | biostudies-literature | 1999 Apr

REPOSITORIES: biostudies-literature