Spidey: A Tool for mRNA-to-Genomic Alignments

Sarah J. Wheelan, Deanna M. Church, James M. Ostell
2001 Genome Research  
We have developed a computer program that aligns spliced sequences to genomic sequences, using local alignment algorithms and heuristics to put together a global spliced alignment. Spidey can produce reliable alignments quickly, even when confronted with noise from alternative splicing, polymorphisms, sequencing errors, or evolutionary divergence. We show how Spidey was used to align reference sequences to known genomic sequences and then to the draft human genome, to align mRNAs to gene
more » ... s, and to align mouse mRNAs to human genomic sequence. We compared Spidey to two other spliced alignment programs; Spidey generally performed quite well in a very reasonable amount of time. 3
doi:10.1101/gr.195301 pmid:11691860 pmcid:PMC311166 fatcat:ibsx3vkkc5g7bjdwp6ovrnysxq