Mokshda Kaushik, Madhurika Sharma, Tirath Raj Singh
Department of Biotechnology & Bioinformatics, JUIT, Waknaghat, Solan (H.P.), India.
ABSTRACT
Enormous amount of genomic and proteomic data is being generated through biological scientific community. There is a continuous need to analyze that data to generate biologically meaningful information. Bioinformatics provided such a platform via combination of biology and computers to help in achieving this significant goal. Here we present a web based application named WISA: (Web server for interactive sequence alignment), which provides the user for various kinds of genomic and proteomic sequence alignment and its analyses. The main purpose of this application is to perform pair-wise as well as multiple sequence alignment for biological sequences. It uses dynamic programming approach for performing the alignment in addition to the usage of several scoring matrices such as identity, transition, and transversion matrices for nucleotide and various versions of PAM and BLOSUM matrices for protein sequences respectively. It also incorporates gap penalty separately for gap initiation and extension therefore it can deal with evolutionary mutational events in a significant way. It will look for global, local and semi-global (end space free) alignments in biological sequences. Semi-global alignment analysis is one of the unique features of this application as it is not available in all available standard alignment programs. WISA also incorporates BLAST for looking homologous sequences related to the user sequence. It can generate MSA (multiple sequence alignment) for multiple inputs of amino acid sequences. MSA will be generated based on profile method of amino acid sequences. Profile matrix will be generated which will further be used to classify data in to various phylogenetic clades. Phylogenetic information will be generated in Newick format to ease the user which can be visualized in any standard evolutionary tree generation program. WISA is being implemented in CGI-PERL with HTML combination in association with Apache as background server. This server allows the user to submit the nucleotide or protein query sequence in FASTA format. User can also upload a FASTA file of the same. Various kinds of options related to nucleotide and amino acid sequences such as usage of myriad matrices is also available for the user. WISA will definitely provide pace to the biological sequence analysis and will also help in generating biologically significant results and information in a user friendly mode. WISA is available for academic use at http://www.bioinfoindia.org/wisa. Read more…
