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

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.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.Protein sequence database searches are routinely employed to detect homologs of the sequence used as a query. However, at present, protein sequence databases are growing exponentially necessitating frequent repetition of searches to find out whether new homologous sequences were added. The analysis of results obtained during such repeated searches may also be tedious and time consuming. The task of manually keeping up with changes in databases becomes unbearable if one is interested in finding new homologs not for a single sequence, but for a few or few dozen sequences. To help cope with the periodic detection of new homologs a number of automatic procedures have been developed including Swiss-Shop [1], DBWatcher [2], BLAST Search Updater [3], ReHAB [4] and DbW [5]. Most of them use BLAST [6], a popular sequence search engine. While BLAST is good in detecting closely related sequences, distant relatives may often escape undetected. Some recent systems for periodic searches use more powerful homology detection tools. For example, ReHAB [4] uses PSI-BLAST and DbW [5] utilizes a collect