Genome-based Biomarkers

One of the major challenges in the field oh health sciences is to design genome based biomarkers, as these biomarkers are more sensitive and accurate than traditional tests. Here, aim is to develop computational tools to predict wide range of biomrakers from genomic information. These resources can be classified in following categories; i) disease identification, ii) disease progression, iii) drug biomarkers.

Webservers for Genome based biomakers  (Raghava's Group)

  1. CancerCSP: Gene expression-based biomarkers for discriminating early and late stage of clear cell renal cancer.
  2. CancerDP: Prioritization of anticancer drugs against a cancer using genomic features of cancer cells.
  3. CancerDR: Cancer drug resistance database.
  4. CancerPDF: Database of cancer-associated peptides of human bodyfluids.
  5. Cancertope: A Platform for Designing Genome-Based Personalized Immunotherapy or Vaccine against Cancer.
  6. CancerUBM: Web bench for analysis of proteomics data and prediction of cancer status of a urine samples.
  7. CCDB: Database of genes involved in Cervix Cancer.
  8. HerceptinR: Information about assays performend to test sensitivity/resistance of Herceptin Antibodies.
  9. HIVcoPRED: Predicting coreceptor used by HIV-1 from Its V3 loop amino acid sequence.
  10. MtbVeb: A webportal for designing vaccine against drug resistant and emerging strains of M. tuberculosis.
  11. RNAcon: A web-server for the prediction and classification of non-coding RNAs.

External Links to web servers developed/mainatined by Indian groups

This section provides URL/links to important websites developed and maintained by Indian researchers. It exclude servers by Raghava's group, which is given in above section. 

  1. 16S classifier: a tool for fast and accurate taxonomic classification of 16S rRNA hypervariable regions in metagenomic datasets.
  2. Bisgoat: Locus minimization in breed prediction using artificial neural network approach.
  3. FBIS: A regional DNA barcode archival & analysis system for Indian fishes.
  4. FmMDb: a versatile database of foxtail millet markers for millets and bioenergy grasses research.
  5. Haemophilus influenzae Genome Database (HIGDB): a single point web resource for Haemophilus influenzae.
  6. IGVBrowser: a genomic variation resource from diverse Indian populations.
  7. IRESPred: Web Server for Prediction of Cellular and Viral Internal Ribosome Entry Site (IRES)
  8. MGEx-Tdb: A novel tissue specific meta:analysis approach for gene expression predictions initiated with a mammalian gene expression testis database.
  9. NGS QC Toolkit: a toolkit for quality control of next generation sequencing data.
  10. PlantRGS: a web server for the identification of most suitable candidate reference genes for quantitative gene expression studies in plants.
  11. QlicRice: a web interface for abiotic stress responsive QTL and loci interaction channels in rice.
  12. RCDB: Renal Cancer Gene Database.
  13. SMBMDb: First whole genome putative microsatellite DNA marker database of sugarbeet for bioenergy and industrial applications.
  14. Streptococcus pneumoniae Genome Database (SPGDB): a database for strain specific comparative analysis of Streptococcus pneumoniae genes and proteins.
  15. TIPMaP: a web server to establish transcript isoform profiles from reliable microarray probes.
  16. WebGeSTer DB: a transcription terminator database.
  17. WNV Typer: a server for genotyping of West Nile viruses using an alignment:free method based on a return time distribution.