[WashU] HMMER
User's Guide


| Dept. of Genetics | WashU | Medical School | Sequencing Center | CGM | IBC|
| Eddy lab | Internal (lab only) | HMMER | PFAM | tRNAscan-SE | Software | Publications |

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Next: Searching a sequence database Up: Tutorial Previous: The programs in HMMER

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).


next up previous contents
Next: Searching a sequence database Up: Tutorial Previous: The programs in HMMER


Direct comments and questions to <eddy@genetics.wustl.edu>