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Bioinformatics Vol. 19 no. 4 2003
Pages 544-545
© 2003 Oxford University Press

Applications Note

Protein family annotation in a multiple alignment viewer

Jason M. Johnson 1,*,{dagger}, Keith Mason 2, Ciamac Moallemi 2, Hualin Xi 1, Shyamal Somaroo 1 and Enoch S. Huang 1,*

1 Pfizer Discovery Technology Center, 620 Memorial Drive, Cambridge, MA 02139, USA
2 Neogenesis Drug Discovery, 840 Memorial Drive, Cambridge, MA 02139, USA

Received on July 11, 2002 ; revised on October 14, 2002 ; accepted on October 25, 2002

Summary: The Pfaat protein family alignment annotation tool is a Java-based multiple sequence alignment editor and viewer designed for protein family analysis. The application merges display features such as dendrograms, secondary and tertiary protein structure with SRS retrieval, subgroup comparison, and extensive user-annotation capabilities.

Availability: The program and source code are freely available from the authors under the GNU General Public License at http://www.pfizerdtc.com

Contact: jason_johnson{at}merck.com enoch_huang{at}cambridge.pfizer.com

* To whom correspondence should be addressed.

{dagger} Present address: Rosetta Inpharmatics, 12040 115th Avenue NE, Kirkland, WA 98034, USA.


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