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Improvement of alignment accuracy utilizing sequentially conserved motifs

DSpace at IIT Bombay

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Field Value
 
Title Improvement of alignment accuracy utilizing sequentially conserved motifs
 
Creator CHAKRABARTI, S
BHARDWAJ, N
ANAND, PA
SOWDHAMINI, R
 
Subject multiple sequence alignment
protein sequences
phylogenetic trees
gap penalties
database
superfamilies
algorithm
 
Description Background: Multiple sequence alignment algorithms are very important tools in molecular biology today. Accurate alignment of proteins is central to several areas such as homology modelling, docking studies, understanding evolutionary trends and study of structure-function relationships. In recent times, improvement of existing progressing programs and implementation of new iterative algorithms have made a significant change in this field. Results: We report an alignment algorithm that combines progressive dynamic algorithm, local substructure alignment and iterative refinement to achieve an improved, user-interactive tool. Large-scale benchmarking studies show that this FMALIGN server produces alignments that, aside from preservation of functional and structural conservation, have accuracy comparable to other popular multiple alignment programs. Conclusions: The FMALIGN server allows the user to fix conserved regions in equivalent position in the alignment thereby reducing the chance of global misalignment to a great extent. FMALIGN is available at http://caps.ncbs.res.in/FMALIGN/Home.html.
 
Publisher BIOMED CENTRAL LTD
 
Date 2011-07-19T01:03:18Z
2011-12-26T12:50:55Z
2011-12-27T05:37:08Z
2011-07-19T01:03:18Z
2011-12-26T12:50:55Z
2011-12-27T05:37:08Z
2004
 
Type Article
 
Identifier BMC BIOINFORMATICS, 5(), -
1471-2105
http://dx.doi.org/10.1186/1471-2105-5-167
http://dspace.library.iitb.ac.in/xmlui/handle/10054/5125
http://hdl.handle.net/10054/5125
 
Language en