Bioinformatic Tools - Introduction
(Continued from previous part...)
blastx compares a
nucleotide query sequence translated in all reading frames against a protein
tblastn compares a
protein query sequence against a nucleotide sequence database dynamically
translated in all reading frames
tblastx compares the
six-frame translations of a nucleotide query sequence against the six-frame
translations of a nucleotide sequence database.
FAST homology search All 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 (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.
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.
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
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, 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
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
Application of Programmes in
JAVA in Bioinformatics:
Since research centers are scattered all around the globe ranging from
private to academic settings, and a range of hardware and OSs are being used,
Java is emerging as a key player in bioinformatics. Physiome Sciences'
computer-based biological simulation technologies and Bioinformatics
Solutions' PatternHunter are two examples of the growing adoption of Java in
Perl in Bioinformatics:
String manipulation, regular expression matching, file parsing, data format
interconversion etc are the common text-processing tasks performed in
bioinformatics. Perl excels in such tasks and is being used by many
developers. Yet, there are no standard modules designed in Perl specifically
for the field of bioinformatics. However, developers have designed several of
their own individual modules for the purpose, which have become quite popular
and are coordinated by the BioPerl project.
The BioJava Project is dedicated to providing Java tools for processing
biological data which includes objects for manipulating sequences, dynamic
programming, file parsers, simple statistical routines, etc.
The BioPerl project is an international association of developers of Perl
tools for bioinformatics and provides an online resource for modules, scripts
and web links for developers of Perl-based software.
(Continued on next part...)