SPIDER: software for protein identification from sequence tags with de novo sequencing error.
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.
Han
Yonghua
Y
Department of Computer Science, University of Western Ontario, London, Canada. yhan2@csd.uwo.ca
Ma
Bin
B
Zhang
Kaizhong
K
D000465:Algorithms; D000595:Amino Acid Sequence; D003627:Data Interpretation, Statistical; D030562:Databases, Protein; D016247:Information Storage and Retrieval / Q000379:methods; D013058:Mass Spectrometry; D008969:Molecular Sequence Data; D011506:Proteins / Q000737:chemistry* / Q000145:classification; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D017386:Sequence Homology, Amino Acid; D016324:Sequence Tagged Sites; D012984:Software
D011506:Proteins