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J Bioinform Comput Biol. 2005 Jun;3(3):697-716.

SPIDER: software for protein identification from sequence tags with de novo sequencing error.

Author information

1
Department of Computer Science, University of Western Ontario, London, Ontario, Canada N6A 5B7, Canada. yhan2@csd.uwo.ca

Abstract

For the identification of novel proteins using MS/MS, de novo sequencing software computes one or several possible amino acid sequences (called sequence tags) for each MS/MS spectrum. Those tags are then used to match, accounting amino acid mutations, the sequences in a protein database. If the de novo sequencing gives correct tags, the homologs of the proteins can be identified by this approach and software such as MS-BLAST is available for the matching. However, de novo sequencing very often gives only partially correct tags. The most common error is that a segment of amino acids is replaced by another segment with approximately the same masses. We developed a new efficient algorithm to match sequence tags with errors to database sequences for the purpose of protein and peptide identification. A software package, SPIDER, was developed and made available on Internet for free public use. This paper describes the algorithms and features of the SPIDER software.

PMID:
16108090
[Indexed for MEDLINE]

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