Scans FASTA files with HMM profiles using HMM search.
Clone the git repository.
Edit search_gelp_hmm.pl and adjust the line with your system as needed:
our $HMMSEARCH_COMMAND = 'hmmsearch';
and you can run search_gelp_hmm:
perl search_gelp_hmm.pl -...
- HMMER 2.3 and above.
- A list of HMM profile files (ending with ".hmm") in a same directory.
- Some FASTA files to scan.
Create a directory four output (optional):
mkdir gelp_hmm_test
Run the script:
perl search_gelp_hmm.pl -d data/hmm -f data/fasta/example_gelp.fa -o ./gelp_hmm_test -a -e 1e-3 -t 8
- Alberto CENCI
- Valentin GUIGNON
- Mathieu ROUARD
Distributed under the GPLv3 License. See LICENSE for more information.
Valentin GUIGNON - v.guignon@cgiar.org
Project Link: https://github.com/guignonv/search_fasta_hmm