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Bioinformatics Vol. 19 no. 2 2003
Pages 307-308
© 2003 Oxford University Press

Applications Note

A profile hidden Markov model for signal peptides generated by HMMER

Zemin Zhang * and William I. Wood

Department of Bioinformatics, Genentech Inc., South San Francisco, CA 94080, USA

Received on June 19, 2002 ; revised on August 15, 2002 ; accepted on August 16, 2002

Summary: Although the HMMER package is widely used to produce profile hidden Markov models (profile HMMs) for protein domains, it has been difficult to create a profile HMM for signal peptides. Here we describe an approach for building a complex model of eukaryotic signal peptides by the standard HMMER package. Signal peptide prediction with this model gives a 95.6% sensitivity and 95.7% specificity.

Availability: The profile HMM for signal peptides, data sets, and the scripts for analyzing data are available for non-commercial use at http://share.gene.com/.

Contact: zemin{at}gene.com

* To whom correspondence should be addressed.


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