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

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3 Author(s)
Yonghua Han ; Western Ontario Univ., London, Ont., Canada ; Bin Ma ; Kaizhong Zhang

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 work describes the algorithms and features of the SPIDER software.

Published in:

Computational Systems Bioinformatics Conference, 2004. CSB 2004. Proceedings. 2004 IEEE

Date of Conference:

16-19 Aug. 2004