This document provides an overview of several freely available bioinformatics tools and open resources. It describes the purpose and function of popular tools for database searching (BLAST, FASTA), sequence alignment (Clustal Omega), visualization (RasMol), molecular dynamics simulation (GROMACS), genome browsing (Ensembl), and protein modeling (MODELLER). These tools are commonly used for tasks like extracting meaningful biological information from databases, comparing sequences, understanding phylogenetic relationships, displaying molecular structures, simulating protein dynamics, and building protein models. The document provides links to each tool's homepage for further information.

1. Publicly available tools
&
open resources
in
BIOINFORMATICS
Arindam Ghosh
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2. 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

3. 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.

4. BLAST homepage

5. Nucleotide BLAST page

6. BLAST result page

7. BLAST result page continuation

8. 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.

9. FASTA homepage

10. FASTA result page

11. FASTA result page

12. 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.

13. Clustal Omega Homepage

14. Clustal Omega result page

15. Clustal Omega result page
contd.

16. 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

17. Different molecular views on RasMol

18. 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.

19. 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

20. Ensemble homepage

21. Ensemble result page

22. Ensemble result page

23. 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.

24. Modeller Homepage

25. 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

26. THANK YOU
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