FASMA: A Service to Format and Analyze Sequences in Multiple Alignments

Multiple sequence alignments are successfully applied in many studies for understanding the structural and functional relations among single nucleic acids and protein sequences as well as whole families. Because of the rapid growth of sequence databases, multiple sequence alignments can often be very large and difficult to visualize and analyze. We offer a new service aimed to visualize and analyze the multiple alignments obtained with different external algorithms, with new features useful for the comparison of the aligned sequences as well as for the creation of a final image of the alignment. The service is named FASMA and is available at http://bioinformatica.isa.cnr.it/FASMA/.

[1]  J. Thompson,et al.  CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.

[2]  Geoffrey J. Barton,et al.  The Jalview Java alignment editor , 2004, Bioinform..

[3]  Ross A. Overbeek,et al.  The genetic data environment an expandable GUI for multiple sequence analysis , 1994, Comput. Appl. Biosci..

[4]  D. Lipman,et al.  Improved tools for biological sequence comparison. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[5]  R. Doolittle,et al.  A simple method for displaying the hydropathic character of a protein. , 1982, Journal of molecular biology.

[6]  Manolo Gouy,et al.  SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny , 1996, Comput. Appl. Biosci..

[7]  Robert C. Edgar,et al.  MUSCLE: a multiple sequence alignment method with reduced time and space complexity , 2004, BMC Bioinformatics.

[8]  A. Michie,et al.  CINEMA--a novel colour INteractive editor for multiple alignments. , 1998, Gene.

[9]  G J Barton,et al.  ALSCRIPT: a tool to format multiple sequence alignments. , 1993, Protein engineering.

[10]  C. Notredame,et al.  Recent progress in multiple sequence alignment: a survey. , 2002, Pharmacogenomics.

[11]  D. Higgins,et al.  T-Coffee: A novel method for fast and accurate multiple sequence alignment. , 2000, Journal of molecular biology.

[12]  Leo Goodstadt,et al.  CHROMA: consensus-based colouring of multiple alignments for publication , 2001, Bioinform..