title: Improvement of alignment accuracy utilizing sequentially conserved motifs.
abstract: 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.
authors.affiliation: National Centre for Biological Sciences (TIFR), Bangalore 560065, India. saikat@ncbs.res.in <saikat@ncbs.res.in>
authors.forename: Saikat
authors.initials: S
authors.lastname: Chakrabarti
authors.forename: Nitin
authors.initials: N
authors.lastname: Bhardwaj
authors.forename: Prem A
authors.initials: PA
authors.lastname: Anand
authors.forename: Ramanathan
authors.initials: R
authors.lastname: Sowdhamini
mesh_terms: D000465:Algorithms; D020816:Amino Acid Motifs / Q000235:genetics; D000595:Amino Acid Sequence / Q000235:genetics; D019985:Benchmarking / Q000379:methods; D017124:Conserved Sequence / Q000235:genetics*; D030562:Databases, Protein; D014644:Genetic Variation; D005914:Globins / Q000737:chemistry; D008969:Molecular Sequence Data; D010455:Peptides / Q000737:chemistry; D017434:Protein Structure, Tertiary; D016415:Sequence Alignment / Q000379:methods / Q000592:standards*; D012984:Software; D012985:Software Design
chemical_list: D010455:Peptides; D005914:Globins