Scripts to functionally annotate genes
Databases needed:
- SwissProt (mmseq2 database formatted)
- TrEMBL (mmseq2 database formatted)
- PFAM_A
- KOFAM
Programs needed:
- mmseq2 (https://github.com/soedinglab/MMseqs2)
- pfam_scan.pl (http://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/PfamScan.tar.gz)
- HMMER-3.1b2 (http://eddylab.org/software/hmmer/hmmer-3.1b2.tar.gz)
- kofamscan (https://github.com/takaram/kofam_scan)
To run annotation:
- Copy control script
run_FuncAnnot_MMseqs.sh
into your working directory - Change the specified variables within the script to those that are appropriate for your system (e.g. path to mmseq2, hmmer, etc.)
- Run the script
./run_FuncAnnot_MMseqs.sh
to start the functional annotation process