Improvement of alignment accuracy utilizing sequentially conserved motifs

Chakrabarti, Saikat ; Bhardwaj, Nitin ; Anand, Prem A. ; Sowdhamini, Ramanathan (2004) Improvement of alignment accuracy utilizing sequentially conserved motifs BMC Bioinformatics, 5 . 167_1-167_12. ISSN 1471-2105

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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

Item Type:Article
Source:Copyright of this article belongs to BioMed Central.
ID Code:61219
Deposited On:15 Sep 2011 03:56
Last Modified:18 May 2016 11:01

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