This page was last updated on Friday, 22-Dec-2023 16:58:08 CST

Installation notes for PfamScan - Dec 22, 2023

Publication

2021 Publication

Current database release

Release notes, shows version of Pfam database

Prerequisites

• Perl modules
  1. $ sudo cpan Moose
  2. BioPerl, or just make the Bio path as shown below
  3. HMMER3

Installation

1. $ cd /programinstallers
2. $ wget -N http://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/PfamScan.tar.gz
3. $ tar -zxvf PfamScan.tar.gz
4. $ cd PfamScan
5. Manually install the Bio::Pfam modules into a directory in the Perl search path
   $ sudo mv Bio /usr/local/lib/site_perl/
6. Manually install the main program
   $ sudo mv pfam_scan.pl /usr/local/bin/
7. Copy README to local web page
   $ cp -puv README ../bioinformatics/programs/pfamscan/README.txt
8. Cleanup
   $ cd /programinstallers ; rm PfamScan -rf
9. Download Pfam data files
   $ sudo mkdir -p /usr/local/bin/hmmer3/data
$ sudo chmod -R 775 /usr/local/bin/hmmer3
10. $ cd /usr/local/bin/hmmer3/data
11. $ wget -N https://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz https://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.dat.gz https://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.seed.gz https://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.full.gz
12. $ gunzip *.gz
    Directory size is 3.5 GBytes after uncompressing
13. $ hmmpress Pfam-A.hmm

    Working...    done.
    Pressed and indexed 14831 HMMs (14831 names and 14831 accessions).
    Models pressed into binary file:   Pfam-A.hmm.h3m
    SSI index for binary model file:   Pfam-A.hmm.h3i
    Profiles (MSV part) pressed into:  Pfam-A.hmm.h3f
    Profiles (remainder) pressed into: Pfam-A.hmm.h3p

14. $ hmmpress Pfam-B.hmm

    Working...    done.
    Pressed and indexed 20000 HMMs (20000 names and 20000 accessions).
    Models pressed into binary file:   Pfam-B.hmm.h3m
    SSI index for binary model file:   Pfam-B.hmm.h3i
    Profiles (MSV part) pressed into:  Pfam-B.hmm.h3f
    Profiles (remainder) pressed into: Pfam-B.hmm.h3p

    Directory size is now 7.2 GBytes
15. For convenience, I modified the pfam_scan.pl program code to make the -dir parameter optional and have a default value, i.e. /usr/local/bin/hmmer3/data
    $ nano /usr/local/bin/pfam_scan.pl
    After line 18 add
    $dir = '/usr/local/bin/hmmer3/data'; # VCRU modification