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. AnnoDUF:
- A Web-Based Tool for Annotating Functions of Proteins Having Domains of Unknown Function
Vishwakarma A, Padmashali N, and Thiyagarajan S
J. Proteome Res., https://doi.org/10.1021/acs.jproteome.4c00251 (2024)
- A web-based tool for structural analysis of point mutations on protein structures.
Sai Tharun Goud, N, Vishwakarma A, Anurag Neelakanteswara, Chandreyee Nandi, Sudha Srinivasan and Saravanamuthu Thiyagarajan
Acta Crystallographica Section F (Under Review)
C. Ex-Ex Primer:
- An experimentally validated tool for designing oligonucleotides spanning spliced nucleic acid regions from multiple species
Balagannavar G, Basavaraju K, Patel K, Sasidharan K, Arumugam TS, Thomas L, Praveena BKG, Raksha HN, Menon R, Acharya KK (2022)
J Biotechnol 343:1-6. doi: 10.1016/j.jbiotec.2021.10.009
D. GREAM:
- A web server to short-list the potentially important genomic repeat elements based on over-/under-representation in specific chromosomal locations such as the gene neighborhoods within or across 17 mammalian species.
Chandrashekar DS, Dey P, Acharya KK (2015)
PLOS One Jul 24;10(7):e0133647.
E. TIPMaP:
- A web server to establish transcript isoform profiles from reliable microarray probes.
Chitturi N, Balagannavar G, Chandrashekar DS, Abinaya S, Srini VS and Acharya KK (2013)
BMC Genomics 14: 922
F. 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)
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).
C. HGEx-ERdb:
- Human Gene Expression database for Endometrial receptivity
Publication: Endometrial receptivity: a revisit to functional genomics studies on human endometrium and creation of HGEx-ERdb.
PLOS One 8(3), e58419