profun (updating database)

Test Environment

Red Hat Enterprise Linux Server release 6.4 (Santiago)

Installation Steps

(A) Download and Unzip profun source package

Create a working directory called 'profun' where all scripts, programs and databases will reside:

Download the profun code:

cd ~/
git clone https://github.com/multicom-toolbox/profun.git
cd profun

(B) Download programs

cd programs
wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/legacy.NOTSUPPORTED/2.2.26/blast-2.2.26-x64-linux.tar.gz
tar -zxvf blast-2.2.26-x64-linux.tar.gz

(C) Download database

mkdir database
cd database

wget ftp://ftp.uniprot.org/pub/databases/uniprot/knowledgebase/uniprot_sprot.dat.gz
gzip -d uniprot_sprot.dat.gz

wget ftp://ftp.uniprot.org/pub/databases/uniprot/knowledgebase/uniprot_sprot.fasta.gz
gzip -d uniprot_sprot.fasta.gz

../../programs/blast-2.2.26/bin/formatdb  -p T -i uniprot_sprot.fasta

(D) Test

(1) Run blast
mkdir -p ./test/2SN3-A/sequence ./test/2SN3-A/Blast_output ./test/2SN3-A/LOG/
perl scripts/blast_search_swiss_prot.pl ./test/2SN3-A.fasta  programs/blast-2.2.26/bin/blastpgp ./test/2SN3-A/sequence ./test/2SN3-A/Blast_output ./database/uniprot_sprot.fasta ./database/uniprot_sprot.dat ./test/2SN3-A/LOG/BLAST.LOG ./database/uniprot_sprot.fasta   

(2) Run prediction
mkdir ./test/2SN3-A/pred
perl bin/R_all_three_methods.pl ./scripts/ ./database/ ./test/2SN3-A/sequence ./test/2SN3-A/Blast_output ./test/2SN3-A/pred