Detection of Alternative Splicing with Phrap

     Sandra Porter, Mark Dilger, Christie Robertson, Todd M. Smith, and Joe Slagel
     Geospiza, Inc. 2442 NW Market St. Seattle, WA 98107 USA

Alternative splicing occurs in several eucaryotic genes. Splice variants are often produced in different tissues, at different stages of development, and can code for proteins with distinct functional properties. Several physical methods have been used to detect alternate splicing including Northern blots, DHPLC analysis, and RT-PCR. Computational methods have largely centered around the use of multiple sequence alignments and BLAST. In this report, we investigate the use of Phrap (www.phrap.org) as a potential tool for detecting alternative splicing. Phrap's combined abilities to assemble genomic sequences and calculate error rates have made it a standard tool in genomic sequencing and SNP detection. Phrap also produces information regarding potential chimeras and deletion clones. In this report, we use the Finch®-Server as a tool to investigate the correspondence between Phrap-identified chimeras and deletion clones and alternately spliced mRNAs.

Plant and Animal Genomics Conference, 2003