Resources: Tools and Databases
IBAB aims to become a world-class institute in the area of bioinformatics and biotechnology, in line with organizations such as the European Bioinformatics Institute. The institute wishes to provide services and tools to the academic and industrial research community. The IBAB faculty and students have developed several databases and tools, which are freely accessible to researchers anywhere.
A. ExPrimer:
- Discontinued, but improved version available; please see Ex-Ex Primer (below). Publication: ExPrimer: to design primers from exon-exon junctions. Bioinformatics, 21(9), 2091-2092 (2005).
B. Ex-Ex Primer, available at http://resource2.ibab.ac.in/exprimer/:
- A primer designing software thoroughly tested experimentally, particularly for junction primers & probes. The tool can also be used for regular primers and probes. (Publication: J Biotechnol. 2021;343:1-6. doi:10.1016/j.jbiotec.2021.10.009)
C. Other tools, coming soon (e.g., a tool for identifying motifs in DNA/RNA based on their position-specific distribution patterns)
A. Tissue-specific mammalian gene expression databases with manual curation of the mass scale expression data
i. MGEx-Tdb:
- Mammalian Gene Expression database for Testis tissue.
Publication: A novel tissue-specific meta-analysis approach for gene expression predictions, initiated with a mammalian gene expression testis database.
BMC Genomics, 11, 467 (2010)
http://resource.ibab.ac.in/MGEx-Tdb/
ii. MGEx-Udb:
- Mammalian Gene Expression Database for Uterus tissue.
Publication: A Mammalian Uterus Database for Expression-Based Cataloguing of Genes across Conditions, Including Endometriosis and Cervical Cancer.
PLoS One, 7, e36776 (2012)
URL: http://resource.ibab.ac.in/MGEx-Udb/
Other similar databases for liver, kidney and prostate tissues, yet to be validated:
MGEx-Ldb, MGEx-Kdb, MGEx-Pdb.
B. piRNA database:
- ‘piRNABank’ is a web analysis system and resource, which provides
comprehensive informationon about piRNAs in human, mouse, rat, zebrafish, platypus and Drosophila.
Publication: piRNABank: a web resource on classified and clustered Piwi-interacting RNAs.
Nucleic Acids Research, 36(1), D173-D177 (2008).
http://pirnabank.ibab.ac.in/