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Published Articles >> Table of Contents >> Abstract
2004 IEEE Computational Systems Bioinformatics Conference (CSB'04)
pp. 206-215
SPIDER: Software for Protein Identification from Sequence Tags with De Novo Sequencing Error
Yonghua Han, University of Western Ontario
Bin Ma, University of Western Ontario
Kaizhong Zhang, University of Western Ontario
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DOI Bookmark: http://doi.ieeecomputersociety.org/10.1109/CSB.2004.1332434
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| Abstract |
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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.
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 Additional Information
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Index Terms- protein identification, de novo sequencing, sequence tags, database search
Citation:
Yonghua Han, Bin Ma, Kaizhong Zhang,
"SPIDER: Software for Protein Identification from Sequence Tags with De Novo Sequencing Error,"
csb,
pp. 206-215,
2004 IEEE Computational Systems Bioinformatics Conference (CSB'04),
2004
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