HMMER

HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs). Compared to BLAST, FASTA, and other sequence alignment and database search tools based on older scoring methodology, HMMER aims to be significantly more accurate and more able to detect remote homologs because of the strength of its underlying mathematical models. In the past, this strength came at significant computational expense, but in the new HMMER3 project, HMMER is now essentially as fast as BLAST.

Note

This is an autogenerated page, more detail including examples may be available for this package. Please see the first section of Software on Stanage

After connecting to Stanage (see Establishing a SSH connection), start an interactive session with the following command:

srun --pty bash -i

A version of HMMER can then be made available with one of the following:

module load HMMER/3.3.2-gompi-2022a

Notes

HMMER was installed using Easybuild, build details can be found in $EBROOTHMMER/easybuild with a given module loaded.

Dependencies for latest version of HMMER