Welcome to

College of Veterinary Science
(Assam Agricultural University, Khanapara, Guwahati - 781022)

Bioinformatics Servers and Tools

 
  1. Biological Databases
    1. Nucleotide Sequences
      1. EMBL, EBI
      2. GenBank, NCBI
      3. DDBJ, Japan
    2. Protein Sequences
      1. SWISS-PROT / UniProtKb
      2. OWL
      3. PIR
    3. Protein Structures
      1. MMDB: Molecular Modeling Database
      2. PDB: Protein Databank (RCSB)
      3. ModBase: Database of Comparative Protein Structure Models
      4. CATH Protein Structure Classification
      5. SCOP Structural Classification of Proteins
    4. Pathways
      1. KEGG (Kyoto Encyclopedia of Genes and Genomes) is a bioinformatics resource for linking genomes to life and the environment
      2. Reactome - a curated knowledgebase of biological pathways
  2. Bioinformatics Services (Online Resources)
    1. National Center for Biotechnology Information (NCBI): Collection public databases for research in computational biology, genome data, and biomedical information
    2. ExPASy: SIB Bioinformatics Resource Portal
    3. European Bioinformatics Institute's Services
    4. SDSC Biology Workbench: A web-based tool for biologists
    5. Ensembl- Software system which produces and maintains automatic annotation on selected eukaryotic genomes
    6. GenePattern - Analysis workflow tool developed to support multidisciplinary genomic research program
    7. BLAST: Analysis tool that finds regions of similarity between biological sequences
    8. ClustalW: ClustalW2 is a general purpose multiple sequence alignment program for DNA & proteins
    9. Primer-BLAST: Provides primers specific to the PCR template sequence
    10. Oligocalc: Oligonucleotide Properties Calculator
    11. Sequence Manipulation Suite: A collection of JavaScript programs for generating, formatting, and analyzing short DNA and protein sequences
    12. In silico PCR amplification
    13. SWISS-MODEL: A fully automated protein structure homology-modeling server
    14. Directory of computer-aided Drug Design tools
    15. SwissDock: A free protein ligand docking web service
    16. ClusPro: Protein-protein docking
    17. PRODRG: A program for generating molecular topologies and unique molecular descriptors from coordinates of small molecules
    18. HotPOINT: Hot Spot Prediction Server for Protein Interfaces
    19. Webcutter - A free, on-line program to help restriction map
    20. NEBcutter - Provides a DNA sequence analysis to find restriction enzymes sites
  
  1. Bioinformatics Software
    1. BioEdit: A biological sequence alignment editor for Windows
    2. MEGA: An integrated tool for sequence alignment, phylogenetic analysis, testing evolutionary hypotheses, etc.
    3. PHYLIP: A free package of programs for inferring phylogenies
    4. RasMol: RasMol is a program for molecular graphics visualisation
    5. UCSF Chimera: Highly extensible, interactive molecular graphics program
    6. VMD: VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics
    7. Modeller: Used for homology or comparative modeling of protein 3D structures
    8. Autodock: A suite of automated docking tools
    9. AutoDockTools (ADT): A graphical front-end for setting up and running AutoDock
    10. NAMD: A parallel molecular dynamics code for large biomolecular systems
    11. GROMACS: A molecular dynamics package for simulations of proteins, lipids and nucleic acids
  2. Bioinformatics Journals
    1. Nucleic Acid Research (8.278)
    2. Bioinformatics (5.323)
    3. Briefings in Bioinformatics (5.298)
    4. Journal of Molecular Biology (3.905)
    5. BMC Bioinformatics (3.02)
    6. Journal of Molecular Graphics and Modelling (2.325)
    7. Journal of Molecular Modeling (1.984)
    8. Journal of Computational Biology (1.5)
    9. PloS Computational Biology
    10. International Journal of Computational Biology and Drug Design
    11. Bioinformation
    12. In Silico Biology
    13. Genome Research
    14. OmicsGateway (Nature)
    15. Proteins: Structure, Function, and Bioinformatics