PepBank - a database of peptides based on sequence text mining and public peptide data sources

Background: Peptides are important molecules with diverse biological functions and biomedical uses. To date, there does not exist a single, searchable archive for peptide sequences or associated al data. Rather, peptide sequences still have to be mined from abstracts and full-length articles, and/or obtained from the fragmented public sources. Description: We have constructed a new database (PepBank), which at the time of writing contains a total of 19,792 individual peptide entries. The database has a web-based user interface with a simple, Google-like search function, advanced text search, and BLAST and Smith-Waterman search capabilities. The major source of peptide sequence data comes from text mining of abstracts. Another component of the database is the peptide sequence data from public sources (ASPD and UniProt). An additional, smaller part of the database is manually curated from sets of full text articles and text mining results. We show the utility of the database in differen...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: Timur Shtatland, Daniel Guettler, Misha Kossodo, Misha Pivovarov, Ralph Weissleder
• Keywords: BMCBI 2007, Databases, Peptide, Peptide Sequences