The IBAB faculty and students have developed a bunch of databases and tools. These are freely accessible to students and researchers anywhere and facilitate ongoing study.
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).
C. MotDet: 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: 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: 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)
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).
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 to access the first tutorials to be hosted, concerning ‘R’.