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Nucleic Acids Research, 2003, Vol. 31, No. 13 3507-3509
© 2003 Oxford University Press

SLAM web server for comparative gene finding and alignment

Simon Cawley*, Lior Pachter1 and Marina Alexandersson2

Affymetrix Inc., 6550 Vallejo St, Suite 100, Emeryville, CA 94608, USA 1 Department of Mathematics, UC Berkeley, USA 2 Fraunhofer-Chalmers Centre, Gothenburg, Sweden

*To whom correspondence should be addressed. Tel: +1 510 428 8534; Fax: +1 510 428 8585; Email: simon_cawley{at}affymetrix.com

SLAM is a program that simultaneously aligns and annotates pairs of homologous sequences. The SLAM web server integrates SLAM with repeat masking tools and the AVID alignment program to allow for rapid alignment and gene prediction in user submitted sequences. Along with annotations and alignments for the submitted sequences, users obtain a list of predicted conserved non-coding sequences (and their associated alignments). The web site also links to whole genome annotations of the human, mouse and rat genomes produced with the SLAM program. The server can be accessed at http://bio.math.berkeley.edu/slam.


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