publicly available tools and open resources in bioinformatics
TRANSCRIPT
Bioinformatics tools
● These are software programs that are designed for extracting the meaningful information from the mass of molecular biology / biological databases & to carry out sequence or structural analysis.
● Major categories of Bioinformatics Tools :● Homology and Similarity Tools● Protein Function Analysis● Structural Analysis● Sequence Analysis
BLAST (http://blast.ncbi.nlm.nih.gov/Blast.cgi)
● Category: Database search
● BLAST=Basic Local Alignment Search Tool
● It finds regions of local similarity between sequences.
● Developed by NCBI
● It compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches.
FASTA (http://www.ebi.ac.uk/Tools/sss/fasta)
●Category: Database search●Alternate to NCBI-BLAST●Suite of programs for searching nucleotide or protein databases with a query sequence. ●FASTX and FASTY translate a nucleotide query for searching a protein database.●TFASTX and TFASTY translate a nucleotide database to be searched with a protein query.
Clustal Omega (http://www.clustal.org/omega/)
●Category: Sequence Alignment●Multiple Sequence Alignment tool (MSA) i.e. it aligns three or more sequences together.●Developed by the CLUSTAL authors at University College Dublin, Ireland●Standalone command line-only tool but is also offered by webservers as of EMBL.●MSA can be used to find conserved sequences and understand phylogenetic relations.
RasMol (http://www.openrasmol.org/)
●Category: Visualisation●Developed by Roger Sayle●Used to display proteins, nucleic acids and small molecules●The program reads in a molecule coordinate file and interactively displays the molecule on the screen in a variety of colour schemes and molecule representations
GROMACS (http://www.gromacs.org/)
●Category: Molecular dynamics (simulation)●GROMACS=GROningen MAchine for Chemical Simulations●Designed for simulations of proteins, lipids and nucleic acids.●Developed in the Biophysical Chemistry department of University of Groningen●GROMACS is operated via the command-line, and can use files for input and output.
Ensembl (http://www.ensembl.org/index.html)
● Category: Genome Browser
● Genome browser is a graphical interface for display of information from a biological database for genomic data.
● It enable researchers to visualize and browse entire genomes (most have many complete genomes) with annotated data including gene prediction and structure, proteins, expression, regulation, variation, comparative analysis, etc
● It is a joint scientific project between the European Bioinformatics Institute and the Wellcome Trust Sanger Institute
MODELLER (http://salilab.org/modeller/)
●Category: Protein Modelling●Used for producing homology models of protein tertiary structures as well as quaternary structures.●MODELLER was originally written and is currently maintained by Andrej Sali at the University of California, San Francisco.
Few more tools....
●Database search- SSEARCH, AB-BLAST, PSI-Search●Sequence alignment- T-Coffee, Sim4, Exonerate, Bioconductor- Biostrings●Visualization- Jmol, PyMOL, Visual Molecular Dynamics●Molecular dynamics- AMBER, CHARMM, Abalone●Genome browser- Argo Genome Browser, Celera Genome Browser, GenomeView●Protein modelling- SWISS-MODEL, WHAT IF, BHAGEERATH-H