title: De novo sequencing and homology searching.
abstract: In proteomics, de novo sequencing is the process of deriving peptide sequences from tandem mass spectra without the assistance of a sequence database. Such analyses have traditionally been performed manually by human experts, and more recently by computer programs that have been developed because of the need for higher throughput. Although powerful, de novo sequencing often can only determine partially correct sequence tags because of imperfect tandem mass spectra. However, these sequence tags can then be searched in a sequence database to identify the exact or a homologous peptide. Homology searches are particularly useful for the study of organisms whose genomes have not been sequenced. This tutorial will present background important to understanding de novo sequencing, suggestions on how to do this manually, plus descriptions of computer algorithms used to automate this process and to subsequently carryout homology-based database searches. This Tutorial is part of the International Proteomics Tutorial Programme (IPTP 1).
authors.affiliation: School of Computer Science, University of Waterloo, Waterloo, ON, Canada N2L 3G1. binma@uwaterloo.ca
authors.forename: Bin
authors.initials: B
authors.lastname: Ma
authors.forename: Richard
authors.initials: R
authors.lastname: Johnson
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D030562:Databases, Protein; D006801:Humans; D008969:Molecular Sequence Data; D010446:Peptide Fragments / Q000032:analysis*; D040901:Proteomics; D020539:Sequence Analysis, Protein; D017386:Sequence Homology, Amino Acid; D012984:Software; D053719:Tandem Mass Spectrometry; D013663:Teaching
chemical_list: D010446:Peptide Fragments
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