The Jalview Java alignment editor

Summary: Multiple sequence alignment remains a crucial method for understanding the function of groups of related nucleic acid and protein sequences. However, it is known that automatic multiple sequence alignments can often be improved by manual editing. Therefore, tools are needed to view and edit multiple sequence alignments. Due to growth in the sequence databases, multiple sequence alignments can often be large and difficult to view efficiently. The Jalview Java alignment editor is presented here, which enables fast viewing and editing of large multiple sequence alignments. Availability:The Jar file and source code for Jalview is freely available via the World Wide Web at http://www.jalview. org. A Jalview mailing list is also available by e-mailing majordomo@sanger.ac.uk with subscribe Jalview in the body

[1]  E. Birney,et al.  Apollo: a sequence annotation editor , 2002, Genome Biology.

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

[3]  Christophe Blanchet,et al.  ANTHEPROT: An integrated protein sequence analysis software with client/server capabilities , 2001, Comput. Biol. Medicine.

[4]  Christophe Combet,et al.  MPSA: integrated system for multiple protein sequence analysis with client/server capabilities , 2000, Bioinform..

[5]  Olivier Poch,et al.  A comprehensive comparison of multiple sequence alignment programs , 1999, Nucleic Acids Res..

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

[7]  J. Thompson,et al.  The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. , 1997, Nucleic acids research.

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

[9]  C. Sander,et al.  A method to predict functional residues in proteins , 1995, Nature Structural Biology.

[10]  N. Saitou,et al.  The neighbor-joining method: a new method for reconstructing phylogenetic trees. , 1987, Molecular biology and evolution.

[11]  M. Sternberg,et al.  Prediction of protein secondary structure and active sites using the alignment of homologous sequences. , 1987, Journal of molecular biology.

[12]  K. Nicholas,et al.  GeneDoc: Analysis and visualization of genetic variation , 1997 .

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