It looks for homologous genes, but unlike BLAST it aims to be more accurate and better to detect remote homologs. Input file is a protein multiple sequence alignment (MSA) from ClustalW.

This tutorial contains:

  • HMMER basics
  • How to use the tool and interpret its output?
  • Questions and practice exercises

For additional documentation visit HMMER documentation section. Material includes a user guide and blog.

In your paper, in addition to cite VectorBase most recent paper when using the site data, tools and/or resources, please also cite hmmer if you use it.

Finn RD, Clements J, Arndt W, Miller BL, Wheeler TJ, Schreiber F, Bateman A, Eddy SR. 2015. HMMER web server: 2015 update. Nucleic Acids Res. 2015 Jul 1;43(W1):W30-8. doi: 10.1093/nar/gkv397.

If you want to discuss any issues raised in this tutorial then please contact the help desk.

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