DeitY supported softwares

1. Institute of Bioinformatics and Applied Biotechnology (IBAB), Biotech Park, Electronics City Phase I, Bengaluru 560100, India

Six databases and five online tools were developed at IBAB, using the support from MeitY, Government of India.

Mammalian gene expression databases:

They would be useful to find out important genes associated with specific conditions in the tissues for which the databases have been developed. Gene expression data-sets have been developed painstakingly for specific conditions. A semi-quantitative meta analysis method has been employed to assign a reliability score for each gene for its expression status every condition and tissue. The score indicates the extent of reproducibility observed across experiments.

Softwares developed:
  • Motif detection tool [MotDet] is designed to analyze the position-specific distribution of DNA motifs in given set of larger sequences.
    Web link: http://resource.ibab.ac.in/cgi-bin/krishna/motdet_version1/motdet.pl

  • Ex-Exprimer: This is designed for designing primers from exon-exon junctions
    Web link: http://resource.ibab.ac.in/cgi-bin/ex-exprimer/exexprimer_home.pl

  • Transcript Isoform Profiles from Microarray Probes tool (TIPMaP) is another way of making a better use of existing data. It uses ‘refined’ probes from microarrays and corresponding raw data to re-derive gene expression patterns and even comment on the expression status of specific alternatively spliced forms of genes.

Some of them are now being published.

2. Dept. of Computational Biology and Bioinformatics, University of Kerala, Trivandrum 695581, Kerala, INDIA

    "HUBCENTRE" Project:

    The hub prediction model, HUBCENTRE, is the first one of its kind which enables the user to know whether a target protein is hub or non-hub based on the primary sequence information alone. The prediction of protein "hubs" was done using physiochemical, thermodynamic and conformational properties of amino acid residues from amino acid sequence. Our prediction results show that meaningful amino acid features can produce signature features for differentiating hubs from non-hubs. The classical classification method, Support Vector Machines (SVM), is used to develop a tool to discriminate between hub and non hub proteins. 

    3. Department of Biotechnology and Bioinformatics (Microbiology Laboratory), North-Eastern Hill University, Shillong 793022, India

    Two online databases were developed, using the support from MeitY, Government of India. These are as below,

      1. North-East Microbial Database (NEMiD)
      The NEMiD is a first of its kind web-based database of microbial diversity in North-East (NE) India which provides information on cultivable/culturable microbes (bacteria, fungi and actinomycetes ) from surface and sub-surface soils across the seven sister states of the region (Arunachal Pradesh, Assam, Manipur, Meghalaya, Mizoram, Nagaland and Tripura ), Sikkim and parts of North Bengal. The database is based on the survey, isolation and characterization carried out for microbes from across the above geographical regions. Information on a particular microbe in the database covers detailed aspects of phylogenetic information on taxonomic outline and classification, morphological, biochemical and molecular characterization, general and cultural characteristics, geographical/location information, history of cultures, preservation details, hazardous information, patent information etc.

      2. Microbial indicator database of Cherrapunjee (MidCherra)
      The database 'MidCherra' is a microbial indicator database of Cherrapunjee and how it differs from that of pristine sacred forests of adjoining areas. It consists of lists of microbes along with their characteristic features especially of fungal and bacterial isolates typical of the degraded /disturbed soils ecosystems of Cherrapunjee and the variations observed in the undisturbed sacred forests.

      4. Bioinformatics Centre, Savitribai Phule, Pune University (SPPU) Maharashtra - 411007, India

        1. ViPs database and BioDB Extractor software were developed under the CoE grant awarded by the MeitY to the Bioinformatics Centre, Savirtibai Phule, University of Pune (SPPU). They are updated regularly and the new versions with added utilities will be launched soon.

        2. BioDB Extractor:

        BioDB Extractor (BDE) provides customized search utilities for widely used Bioinformatics databases through web-based user interface.  The databases covered in BDE include EMBL-ENA, UniProtKB, PDB, KEGG, Drugbank & DSSP. The user can search & retrieve the subsets of data from entry file/s present in various databases. Even though many search utilities available on WWW for various Bioinformatics databases, these are not fully customizable for search and retrieval of specific subsets of data in batch mode. BDE is developed for customized searches and retrieval of subsets of data, for the purpose of desired downstream processing.

      5. Dept. of Bioinformatics Bharathiar University, Coimbatore, Tamil Nadu-641 046. India.

      The following are the three text mining software developed by our group with web links.

        1. Protein interaction miner: PPInterFinder - A web Server for Minining Human PPI from Biomedical Literature

        2. Protein Name Normalization: ProNormz A web Server for Human Proteins and Protein Kinases Normalization

        3. Protein Entity tagger:
        Web link: www.biominingbu.org:8080/NAGGNER

      6. NIPER, S.A.S. Nagar, Punjab