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.

 

Tools

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

C. MotDet: A DNA motif analysis tool, particularly designed for analyzing core promoter motifs.

 

Databases

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)

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).