Bioinformatics Advance Access originally published online on January 22, 2004
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Bioinformatics 20(3) © Oxford University Press 2004; all rights reserved.
Applications Note |
The Jalview Java alignment editor
1 The Wellcome Trust Sanger Institute and 2 The European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, UK, 3 School of Life Sciences, University of Dundee, Dow St, Dundee, DD1 5EH, UK and 4 The Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, UK
Received on April 16, 2003
; revised on August 4, 2003
; accepted on August 6, 2003
Advance Access Publication January 22, 2004
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{at}sanger.ac.uk with subscribe Jalview in the body of the mail.
Contact: michele{at}sanger.ac.uk
* To whom correspondence should be addressed.
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 M. E. Ortiz-Soto, M. Rivera, E. Rudino-Pinera, C. Olvera, and A. Lopez-Munguia Selected mutations in Bacillus subtilis levansucrase semi-conserved regions affecting its biochemical properties Protein Eng. Des. Sel., October 1, 2008; 21(10): 589 - 595. [Abstract] [Full Text] [PDF]
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H. Demirci, S. T. Gregory, A. E. Dahlberg, and G. Jogl Crystal Structure of the Thermus thermophilus 16 S rRNA Methyltransferase RsmC in Complex with Cofactor and Substrate Guanosine J. Biol. Chem., September 26, 2008; 283(39): 26548 - 26556. [Abstract] [Full Text] [PDF]
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Y. Yamada, H. Y. Wang, M. Fukuzawa, G. J. Barton, and J. G. Williams A new family of transcription factors Development, September 15, 2008; 135(18): 3093 - 3101. [Abstract] [Full Text] [PDF]
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M. P. Westbye, E. Feyzi, P. A. Aas, C. B. Vagbo, V. A. Talstad, B. Kavli, L. Hagen, O. Sundheim, M. Akbari, N.-B. Liabakk, et al. Human AlkB Homolog 1 Is a Mitochondrial Protein That Demethylates 3-Methylcytosine in DNA and RNA J. Biol. Chem., September 5, 2008; 283(36): 25046 - 25056. [Abstract] [Full Text] [PDF]
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R. A. Studer, S. Penel, L. Duret, and M. Robinson-Rechavi Pervasive positive selection on duplicated and nonduplicated vertebrate protein coding genes Genome Res., September 1, 2008; 18(9): 1393 - 1402. [Abstract] [Full Text] [PDF]
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A. B. Prasad, M. W. Allard, NISC Comparative Sequencing Program, and E. D. Green Confirming the Phylogeny of Mammals by Use of Large Comparative Sequence Data Sets Mol. Biol. Evol., September 1, 2008; 25(9): 1795 - 1808. [Abstract] [Full Text] [PDF]
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 I. Lasry, B. Berman, R. Straussberg, Y. Sofer, H. Bessler, M. Sharkia, F. Glaser, G. Jansen, S. Drori, and Y. G. Assaraf A novel loss-of-function mutation in the proton-coupled folate transporter from a patient with hereditary folate malabsorption reveals that Arg 113 is crucial for function Blood, September 1, 2008; 112(5): 2055 - 2061. [Abstract] [Full Text] [PDF]
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C. G. Grummitt, F. M. Townsley, C. M. Johnson, A. J. Warren, and M. Bycroft Structural Consequences of Nucleophosmin Mutations in Acute Myeloid Leukemia J. Biol. Chem., August 22, 2008; 283(34): 23326 - 23332. [Abstract] [Full Text] [PDF]
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S. B. Ozturk and T. G. Kinzy Guanine Nucleotide Exchange Factor Independence of the G-protein eEF1A through Novel Mutant Forms and Biochemical Properties J. Biol. Chem., August 22, 2008; 283(34): 23244 - 23253. [Abstract] [Full Text] [PDF]
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