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Tools in Bioinformatics

This document discusses various bioinformatics tools used for analyzing genomic and proteomic data. It describes categories of tools including homology and similarity tools, protein functional analysis tools, sequence analysis tools, and structural analysis tools. Specific tools discussed include BLAST, FASTA, EMBOSS, ClustalW, RasMol, PROSPECT, PatternHunter, and COPIA.

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Jane Guiron Aballa
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137 views

Tools in Bioinformatics

This document discusses various bioinformatics tools used for analyzing genomic and proteomic data. It describes categories of tools including homology and similarity tools, protein functional analysis tools, sequence analysis tools, and structural analysis tools. Specific tools discussed include BLAST, FASTA, EMBOSS, ClustalW, RasMol, PROSPECT, PatternHunter, and COPIA.

Uploaded by

Jane Guiron Aballa
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© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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Tools used in

Bioinformatics

Zaifful Gani
Major categories of
Bioinformatics Tools
There are both standard and customized
products to meet the requirements of
particular projects. There are data-mining
software that retrieve data from genomic
sequence databases and also visualization
tools to analyze and retrieve information
from proteomic databases. These can be
classified as homology and similarity tools,
protein functional analysis tools, sequence
analysis tools and miscellaneous tools.
Homology and
Similarity Tools
Homologous sequences are sequences that
are related by divergence from a common
ancestor. Thus the degree of similarity
between two sequences can be measured
while their homology is a case of being either
true of false. This set of tools can be used to
identify similarities between novel query
sequences of unknown structure and
function and database sequences whose
structure and function have been elucidated.
Protein Function
Analysis
This group of programs allow you to
compare your protein sequence to
the secondary (or derived) protein
databases that contain information on
motifs, signatures and protein
domains. Highly significant hits
against these different pattern
databases allow you to approximate
the biochemical function of your
query protein.
Structural Analysis

This set of tools allow you to compare


structures with the known structure
databases. The function of a protein is
more directly a consequence of its
structure rather than its sequence
with structural homologs tending to
share functions. The determination of
a protein's 2D/3D structure is crucial
in the study of its function.
Sequence Analysis

This set of tools allows you to carry


out further, more detailed analysis on
your query sequence including
evolutionary analysis, identification of
mutations, hydropathy regions, CpG
islands and compositional biases. The
identification of these and other
biological properties are all clues that
aid the search to elucidate the
specific function of your sequence.
Some Examples of
Bioinformatics Tools
BLAST

BLAST ( Basic Local Alignment Search


Tool) comes under the category of
homology and similarity tools. It is a
set of search programs designed for
the Windows platform and is used to
perform fast similarity searches
regardless of whether the query is for
protein or DNA.
BLAST

Comparison of nucleotide sequences


in a database can be performed. Also
a protein database can be searched to
find a match against the queried
protein sequence. NCBI has also
introduced the new queuing system
to BLAST (Q BLAST) that allows users
to retrieve results at their
convenience and format their results
multiple times with different
formatting options.
FASTA
FAST homology search A ll sequences
. An alignment program for protein
sequences created by Pearsin and
Lipman in 1988. The program is one
of the many heuristic algorithms
proposed to speed up sequence
comparison. The basic idea is to add a
fast prescreen step to locate the
highly matching segments between
two sequences, and then extend
these matching segments to local
alignments using more rigorous
algorithms such as Smith-Waterman.
EMBOSS
EMBOSS (European Molecular
Biology Open Software Suite) is a
software-analysis package. It can
work with data in a range of formats
and also retrieve sequence data
transparently from the Web.
Extensive libraries are also provided
with this package, allowing other
scientists to release their software as
open source. It provides a set of
sequence-analysis programs, and also
supports all UNIX platforms.
Clustalw
It is a fully automated
sequence alignment tool for
DNA and protein
sequences. It returns the
best match over a total
length of input sequences,
be it a protein or a nucleic
acid.
RasMol
It is a powerful research
tool to display the
structure of DNA,
proteins, and smaller
molecules. Protein
Explorer, a derivative of
RasMol, is an easier to
use program.
PROSPECT
PROSPECT (PROtein
Structure Prediction and
Evaluation Computer
ToolKit) is a protein-
structure prediction system
that employs a
computational technique
called protein threading to
construct a protein's 3-D
model.
PatternHunter
PatternHunter, based on Java, can
identify all approximate repeats in a
complete genome in a short time
using little memory on a desktop
computer. Its features are its
advanced patented algorithm and
data structures, and the java language
used to create it. The Java language
version of PatternHunter is just 40
KB, only 1% the size of Blast, while
offering a large portion of its
functionality.
COPIA
COPIA (COnsensus Pattern
Identification and Analysis) is a
protein structure analysis tool for
discovering motifs (conserved
regions) in a family of protein
sequences. Such motifs can be then
used to determine membership to the
family for new protein sequences,
predict secondary and tertiary
structure and function of proteins and
study evolution history of the
sequences.
Thank you.

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