About Re-searcher

Re-searcher is an open source system for recurrent detection and reporting of new homologs in protein sequence databases. The system uses PSI-BLAST as the search engine, is highly configurable and supports multiple users. Re-searcher has been developed at the Institute of Biotechnology, Laboratory of Bioinformatics, Vilnius, Lithuania.

To use Re-searcher, enter new protein sequence (query) and choose PSI-BLAST parameters for the search. Each user has his own sequence (query) list for which PSI-BLAST searches are executed periodically.

Quick Installation Guide

Use the following instructions to install the Re-searcher for searches within the NCBI databases. If you encounter problems or you need additional explanation refer to the documentation.

1. Download and install Java Runtime Environment. In Linux, set your $PATH variable to contain the folder of java executable.
2. Download and extract Re-searcher to desired location on your file system.
3. To start Researcher in Windows run the researcher/bin/researcher.bat.
   To Start Researcher in Linux use the following command: "researcher/bin/researcher console".
4. After starting, follow this link to start using Re-searcher http://localhost:8080/Researcher/app.

Configuring Local PSI-BLAST Searches

In order to run searches on a local server you need to do some configuration. Local server must have PSI-BLAST installed and ssh access enabled. To configure Re-searcher's access to the local server:

1. Login to Re-searcher as administrator (initially, user name and password both have value "admin"). Follow "Configuration" link in the main menu.
2. Fill in PSI-BLAST server options. For help on PSI-BLAST server options click the questionmark in the Re-searcher's window or refer to the documentation.

Configuring Email Notifications

To enable email notifications:

1. Login to Re-searcher as administrator (initially, user name and password both have value "admin"). Follow "Configuration" link in the main menu.
2. Fill in email notification options. For help on PSI-BLAST server options click the questionmark in the Re-searcher's window or refer to the documentation.