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Bioinformatics Vol. 19 no. 5 2003
Pages 675-676
© 2003 Oxford University Press

Applications Note

ASAP: automated sequence annotation pipeline for web-based updating of sequence information with a local dynamic database

Andrew Kossenkov 1,2, Frank J. Manion 2, Eugene Korotkov 3, Thomas D. Moloshok 2 and Michael F. Ochs 2,*

1 Cybernetics Department, Moscow Engineering Physics Institute, Moscow, Russian Federation
2 Department of Information Science and Technology, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
3 Center of Bioengineering, Russian Academy of Sciences, Moscow 117312, Russian Federation

Received on July 27, 2002 ; revised on October 22, 2002 ; accepted on November 12, 2002

Summary: The automated sequence annotation pipeline (ASAP) is designed to ease routine investigation of new functional annotations on unknown sequences, such as expressed sequence tags (ESTs), through querying of web-accessible resources and maintenance of a local database. The system allows easy use of the output from one search as the input for a new search, as well as the filtering of results. The database is used to store formats and parameters and information for parsing data from web sites. The database permits easy updating of format information should a site modify the format of a query or of a returned web page.

Availability: Source code is available under the GNU public license at http://bioinformatics.fccc.edu/

Contact: av_kossenkov{at}fccc.edufj_manion{at}fccc.edukatrin22{at}mtu-net.rutd_moloshok{at}fccc.edum_ochs{at}fccc.edu

* To whom correspondence should be addressed.


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