A Generalized Hidden Markov Model for the Recognition of Human Genes in DNA . EcoParse is a mailserver for finding genes in E. coli DNA that uses a Hidden Markov Model. An abstract and a full paper are available.
Postscript is also available.
A more detailed presentation of SAM-T98 than the Proteins paper. Three papers on the Visualization and Sonification of Protein Structure Sequence Alignments Neural-network protein structure prediction A short poster presentation. Official journal web site. Regularizers for Estimating Distributions of Amino Acids from Small Samples.