Spidey: A Tool for mRNA-to-Genomic Alignments | Zendy

Sarah J. Wheelan | Zendy; Deanna M. Church | Zendy; James M. Ostell | Zendy

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Spidey: A Tool for mRNA-to-Genomic Alignments

Author(s) -

Sarah J. Wheelan,

Deanna M. Church,

James M. Ostell

Publication year - 2001

Publication title -

genome research

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 9.556

H-Index - 297

eISSN - 1549-5469

pISSN - 1088-9051

DOI - 10.1101/gr.195301

Subject(s) - biology , computational biology , genetics , human genome , genome , sequence (biology) , rna splicing , alignment free sequence analysis , heuristics , multiple sequence alignment , genomics , alternative splicing , gene , sequence alignment , exon , rna , computer science , peptide sequence , operating system

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 clusters, 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.

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