Objective: To provide the customized search utilities for widely used Bioinformatics databases through a single web-based user interface.

Background: We have developed a system named as BioDB Extractor (BDE) in which user can search & retrieve the subsets of data from entry file/s present in various databases. Even though many search utilities available on WWW for various Bioinformatics databases, these are not fully customizable for search and retrieval of specific subsets of data in batch mode. BDE is developed for customized searches and retrieval of subsets of data, for the purpose of  desired downstream processing.

Salient features:

  1. 1 BDE includes widely used various Bioinformatics databases such as nucleotide databases (GenBank, ENA, DDBJ), protein sequence database (Uniprot), structure database (PDB), pathway database (KEGG), drug molecules database( DrugBank), DSSP etc.

  2. 2 Users need not download the entire data files from respective databases which save the storage space on local disk of users computer as well as time.

  3. 3 Provide the facility to retrieve desired subsets of data from respective databases in customized manner & download it.

  4. 4 Customizable batch retrieval system for all included databases.

  5. 5 Users need not to write any script to parse the subsets of data from database entry file/s.

  6. 6 Very simple interface to upload input files & download output files.

Technical details: BDE is developed on the windows operating system and Apache HTTP Server (Version-2.2.21) is used as the Web server. HTML, CSS, PHP, and JAVA scripts are used for developing the web pages (Interfaces). Perl, Perl-LWP, Perl-cgi, SOAP::WSDL are used for data retrieval & to build the search utility.

Bioinformatics centre, University of Pune, India