Publicly available tools&

open resourcesin

BIOINFORMATICS

Arindam Ghosh

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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.

BLAST homepage

Nucleotide BLAST page

BLAST result page

BLAST result page continuation

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.

FASTA homepage

FASTA result page

FASTA result page

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.

Clustal Omega Homepage

Clustal Omega result page

Clustal Omega result page contd.

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

Different molecular views on RasMol

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

Ensemble homepage

Ensemble result page

Ensemble result page

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.

Modeller Homepage

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

THANK YOU

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