Genome Analysis QPRIMER: A Quick Web-based Application for Designing Con- served PCR Primers from Multigenome Alignments

Summary: We have developed a quick web-based application for designing conserved genomic PCR and RT-PCR primers from mul-tigenome alignments targeting specific exons or introns. We used Pygr (The Python Graph Database Framework for Bioinformatics) to query intervals from multigenome alignments, which gives us less than a millisecond access to any intervals of any genome within multigenome alignments. PRIMER3 was used to extract optimal primers from a gene of interest. QPRIMER creates an electronic genomic PCR image from a set of conserved primers as well as summary pages for primer alignments and products. QPRIMER supports human, mouse, rat, chicken, dog, zebrafish, and fruit fly