Email updates

Keep up to date with the latest news and content from BMC Bioinformatics and BioMed Central.

Open Access Open Badges Software

Improvement of alignment accuracy utilizing sequentially conserved motifs

Saikat Chakrabarti1, Nitin Bhardwaj2, Prem A Anand3 and Ramanathan Sowdhamini1*

Author affiliations

1 National Centre for Biological Sciences (TIFR), Bangalore 560065, India

2 Department of Chemical Engineering, Indian Institute of Technology, Mumbai, India

3 International Institute of Information Technology (MSIT), Hyderabad, India

For all author emails, please log on.

Citation and License

BMC Bioinformatics 2004, 5:167  doi:10.1186/1471-2105-5-167

Published: 28 October 2004



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.


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.


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 webcite