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.
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.
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.
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
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