EXPEDITOR: A PIPELINE FOR DESIGNING PIG PRIMERS USING HUMAN GENE STRUCTURE AND PIG EST INFORMATION

¹ Department of Animal Science, Center for Integrated Animal Genomics, Iowa State University, 2255 Kildee Hall, Ames, IA 50011, U.S.A.

The candidate gene and positional candidate gene approaches for identification of genes associated with economically important traits in farm animals have great utility. These approaches have the opportunity to use the abundant sequence and mapping information from human genome studies. To facilitate a rapid PCR-based approach to study candidate genes in pigs, we have created a software pipeline, Expeditor, to enable a streamlined primer design. This pipeline uses proper human gene structure and pig coding sequence information in order to design primers that can amplify gene fragments from pig genomic DNA. The Expeditor is designed to take the Ensembl ExonView sequences as its standard input. NCBI Blast is employed to find the best matches of pig sequences to each exon in the human gene sequence. When a proper match is found, the exon is replaced with pig sequence. The process is repeated until all exons are evaluated. The new sequence template is then passed to Primer3 for primer design. We have designed a web form for input of raw data as well as user defined parameter values for blast stringency and Primer3. In addition, minimum matched length and acceptable score values were added to filter for acceptable blast results. Upon each successful run, five kinds of results are produced and saved for users to retrieve through web links. This software helps to relieve researchers from tedious manual operations and reduces the chance of errors by more conventional approaches.