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polyphen-software

PolyPhen-2

PolyPhen-2 (Polymorphism Phenotyping v2) is a software tool which predicts possible impact of amino acid substitutions on the structure and function of human proteins using straightforward physical and evolutionary comparative considerations.

Information

Usage

See versions of polyphen which are available:

$ module avail polyphen

Load polyphen:

$ module load polyphen

Installation

Notes from the sysadmin during installation:

$ scl enable devtoolset-3 bash
$ module load perl/5.22.3
$ sudo chown -R aorth:aorth /export/apps/perl/5.22.3
$ cpanm XML::Simple LWP::Simple DBD::SQLite
$ cd /tmp
$ wget http://genetics.bwh.harvard.edu/pph2/dokuwiki/_media/polyphen-2.2.2r405c.tar.gz
$ tar xf polyphen-2.2.2r405c.tar.gz
$ wget ftp://genetics.bwh.harvard.edu/pph2/bundled/polyphen-2.2.2-databases-2011_12.tar.bz2
$ wget ftp://genetics.bwh.harvard.edu/pph2/bundled/polyphen-2.2.2-alignments-mlc-2011_12.tar.bz2
$ wget ftp://genetics.bwh.harvard.edu/pph2/bundled/polyphen-2.2.2-alignments-multiz-2009_10.tar.bz2
$ tar xf polyphen-2.2.2-databases-2011_12.tar.bz2
$ tar xf polyphen-2.2.2-alignments-mlc-2011_12.tar.bz2
$ tar xf polyphen-2.2.2-alignments-multiz-2009_10.tar.bz2
$ cd polyphen-2.2.2
$ wget ftp://ftp.ncbi.nih.gov/blast/executables/blast+/2.2.31/ncbi-blast-2.2.31+-x64-linux.tar.gz
$ tar xf ncbi-blast-2.2.31+-x64-linux.tar.gz
$ mv ncbi-blast-2.2.31+/* blast
$ rm -rf ncbi-blast-2.2.31+*
$ wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/blat -O bin/blat
$ wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/twoBitToFa -O bin/twoBitToFa
$ chmod +x bin/blat bin/twoBitToFa
$ cd nrdb
$ wget ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/uniref/uniref100/uniref100.fasta.gz
$ gunzip uniref100.fasta.gz
$ ../update/format_defline.pl uniref100.fasta >uniref100-formatted.fasta
$ ../blast/bin/makeblastdb -in uniref100-formatted.fasta -dbtype prot -out uniref100 -parse_seqids
$ rm -f uniref100.fasta uniref100-formatted.fasta
$ cd ..
$ rsync -rltv --delete-after --port=33444 rsync.wwpdb.org::ftp/data/structures/divided/pdb/ wwpdb/divided/pdb/
$ rsync -rltv --delete-after --port=33444 rsync.wwpdb.org::ftp/data/structures/all/pdb/ wwpdb/all/pdb/
$ sleep 8h && rsync -rltvz --delete-after rsync://rsync.cmbi.ru.nl/dssp/ dssp/
$ cd ..
$ sudo mkdir /export/apps/polyphen
$ sudo chown aorth:aorth /export/apps/polyphen
$ cp -r polyphen-2.2.2 /export/apps/polyphen/2.2.2
$ export PPH=/export/apps/polyphen/2.2.2
$ cd $PPH/src
$ make download
$ make clean
$ make
$ make install
$ cd $PPH
$ ./configure
$ find $PPH/scratch -type d -exec chmod 777 {} \;
$ find $PPH/scratch -type d -exec chmod +t {} \;
$ sudo chown -R root:root $PPH

Note that this can take nearly 200GB of space and many hours to download, expand, and process all the data files.

polyphen-software.txt · Last modified: 2017/04/01 18:56 by aorth