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.

  • Tools
  • Databases
  • Educational resources

A. ExPrimer:

  1. 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:

  1. ExPrimer reconstructed with improved features (for designing primers from novel exon-exon junctions).

C. MotDet:

  1. A DNA motif analysis tool, particularly designed for analyzing core promoter motifs.

A. Tissue-specific mammalian gene expression databases with manual curation of the mass scale expression data

i. MGEx-Tdb:

  1. 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)

ii. MGEx-Udb:

  1. 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)
    Other similar databases for liver, kidney and prostate tissues, yet to be validated:
    MGEx-Ldb, MGEx-Kdb, MGEx-Pdb.

B. piRNA database:

  1. ‘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).

Dr. Srivatsan is developing free tutorials on computer languages, statistical methods and algorithms that are useful for creating innovative analysis tools for computational biology. Click here (Link: http://www.countbio.com/index.html) to access the first tutorials to be hosted, concerning ‘R’.