Search FASTA HMM

Scans FASTA files with HMM profiles using HMM search.

Getting Started

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 -...

Prerequisites

• HMMER 2.3 and above.
• A list of HMM profile files (ending with ".hmm") in a same directory.
• Some FASTA files to scan.

Usage

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

Contributing

• Alberto CENCI
• Valentin GUIGNON
• Mathieu ROUARD

License

Distributed under the GPLv3 License. See LICENSE for more information.

Contact

Valentin GUIGNON - v.guignon@cgiar.org

Project Link: https://github.com/guignonv/search_fasta_hmm

Acknowledgments

HMMER