DBToolkit: processing protein databases for peptide-centric proteomics

Bioinformatics. 2005 Sep 1;21(17):3584-5. doi: 10.1093/bioinformatics/bti588. Epub 2005 Jul 19.

Abstract

DBToolkit is a user-friendly, easily extensible tool that allows the processing of protein sequence databases to peptide-centric sequence databases. This processing is primarily aimed at enhancing the useful information content of these databases for use as optimized search spaces for efficient identification of peptide fragmentation spectra obtained by mass spectrometry. In addition, DBToolkit can be used to reliably solve a range of other typical tasks in processing sequence databases.

Availability: DBToolkit is open source under the GNU GPL license. The source code, full user and developer documentation and cross-platform binaries are freely downloadable from the project website at http://genesis.UGent.be/dbtoolkit/

Contact: lennart.martens@UGent.be

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Database Management Systems*
  • Databases, Protein*
  • Information Storage and Retrieval / methods
  • Peptide Mapping / methods*
  • Peptides / analysis
  • Peptides / chemistry*
  • Proteomics
  • Sequence Alignment / methods*
  • Sequence Analysis, Protein / methods*
  • Software*

Substances

  • Peptides