Re-searcher: a system for recurrent detection of homologous protein sequences

BMC Bioinformatics. 2008 Jun 27;9:296. doi: 10.1186/1471-2105-9-296.

Abstract

Background: Sequence searches are routinely employed to detect and annotate related proteins. However, a rapid growth of databases necessitates a frequent repetition of sequence searches and subsequent analysis of obtained results. Although there are several automatic systems available for executing periodical sequence searches and reporting results, they all suffer either from a lack of sensitivity, restrictive database choice or limited flexibility in setting up search strategies. Here, a new sequence search and reporting software package designed to address these shortcomings is described.

Results: Re-searcher is an open-source highly configurable system for recurrent detection and reporting of new homologs for the sequence of interest in specified protein sequence databases. Searches are performed using PSI-BLAST at desired time intervals either within NCBI or local databases. In addition to searches against individual databases, the system can perform "PDB-BLAST"-like combined searches, when PSI-BLAST profile generated during search against the first database is used to search the second database. The system supports multiple users enabling each to separately keep track of multiple queries and query-specific results.

Conclusions: Re-searcher features a large number of options enabling automatic periodic detection of both close and distant homologs. At the same time it has a simple and intuitive interface, making the analysis of results even for a large number of queries a straightforward task.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Databases, Protein
  • Humans
  • Proteins / chemistry*
  • Proteins / genetics
  • Sequence Analysis, Protein*
  • Sequence Homology
  • Software*

Substances

  • Proteins