HMMER User's Guide

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Files used in the tutorial

The subdirectory /Demos in the HMMER distribution contains the files used in the tutorial, as well as a number of examples of various file formats that HMMER reads. The important files for the tutorial are:

globins50.msf

An MSF format alignment file of 50 aligned globin sequences.

globins630.fa

A FASTA format file of 630 unaligned globin sequences.

fn3.slx

A SELEX format alignment file of fibronectin type III domains.

rrm.slx

A SELEX format alignment file of RNA recognition motif domains.

pkinase.slx

A SELEX format alignment file of protein kinase catalytic domains.

Artemia.fa

A FASTA file of brine shrimp globin, which contains nine tandemly repeated globin domains.

7LES_DROME

A SWISSPROT file of the Drosophila Sevenless sequence, a receptor tyrosine kinase with multiple domains.

Create a new directory that you can work in, and copy all the files in Demos there. I'll assume for the following examples that you've installed the HMMER programs in your path; if not, you'll need to give a complete path name to the HMMER programs (e.g. something like /usr/people/eddy/ hmmer-2.0/hmmbuild instead of just hmmbuild).