NDLI: Phylogenetic analysis of some leguminous trees using CLUSTALW2 bioinformatics tool

Content Provider	IEEE Xplore Digital Library
Author	Patel, S. Panchal, H. Anjaria, K.
Copyright Year	2012
Description	Author affiliation: G.H. Patel Post Graduate Department of Computer, Science & Technology, Sardar Patel University., Vallabh Vidyanagar, Dist: Anand, Gujarat, India (Patel, S.; Panchal, H.) \|\| Department of Biology, Shri R. K. Parikh Arts and Science College, Gujarat University., Petlad, Dist : Anand, Gujarat, India (Anjaria, K.)
Abstract	A multiple sequence alignment (MSA) is a sequence alignment of three or more biological sequences, generally for Protein. MSA has wide range of applications and to cite few of them such as phylogenetic analysis, protein pattern identification, protein domain identification, prediction of protein structure, structural similarity of amino acids and to get evolutionary similarity. ClustalW2 is a general purpose global multiple sequence alignment program for proteins. It produces biologically meaningful multiple sequence alignments of divergent sequences. The output from ClustalW2 shows the best match for the selected sequences and lines up them in such a way that the identities, similarities and differences can be easily understood. Evolutionary relationships can be seen by creating Cladograms or Phylograms. Firstly, individual weights are assigned to each sequence in a partial alignment in order to down-weight near-duplicate sequences and up-weight the most divergent ones. Secondly, amino acid substitution matrices are varied at different alignment stages according to the divergence of the sequences to be aligned. Thirdly, residue-specific gap penalties and locally reduced gap penalties in hydrophilic regions encourage new gaps in potential loop regions rather than regular secondary structure. Fourthly, positions in early alignments where gaps have been opened receive locally reduced gap penalties to encourage the opening up of new gaps at these positions. In this paper, protein sequences of few legume species from UNIPROT database were taken and focused on MSA for protein sequences for these tree species of family Leguminosae, where ClustalW2 tool have used to generate biological data. The results are discussed with the help of Cladograms and Phylograms for selected tree species.
Starting Page	917
Ending Page	921
File Size	2749768
Page Count	5
File Format	PDF
ISBN	9781467327466
e-ISBN	9781467327473
e-ISBN	9781467327442
DOI	10.1109/BIBMW.2012.6470264
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2012-10-04
Publisher Place	USA
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Proteins Protein engineering Vegetation MSA- Multiple sequence alignment Educational institutions Phylogeny Bioinformatics
Content Type	Text
Resource Type	Article

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