1. Download the two trained model files: gpcr.mod, ATH1.pep2.mlib 2. You need to have the SAM package on your own machine. Go to the SAM web site at UCSC. You need to obtain the free academic license before you can download the software. 3. Once the software is installed, type this command line: "hmmscore test -db fasta.txt -i gpcr.mod -modellibrary ATH1.pep2.mlib -dbsize 28952" "test" is the "run" name (this name is used to generate the result file, "test.1.gpcr.mod.dist", "-i gpcr.mod" specifies the model file, "-modellibrary ATH1.pep2.mlib" is also required to specify the model, "-db fasta.txt" specifies your sequence file (in FASTA format), "-dbsize 28951" is to obtain the e-value equivalent to the search against the original ATH1.pep2 database (28951 is the number of sequences). For more details, please read the SAM User Guide.