Bioinformatic Tools - Introduction

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·                  blastx compares a nucleotide query sequence translated in all reading frames against a protein sequence database

·                  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.

FASTA:
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:
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.

Application of Programmes in Bioinformtics:

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 bioinformatics.

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.

Bioinformatics Projects:

BioJava:
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.

BioPerl:
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.

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