[BioTools] Polyphen

Downloads

- http://genetics.bwh.harvard.edu/pph2/dokuwiki/downloads

Installation

$ sudo /BiO/apps/perl-5.24.0/bin/perl -MCPAN "-e install 'XML::Simple'"

$ sudo /BiO/apps/perl-5.24.0/bin/perl -MCPAN "-e install 'LWP::Simple'"

$ sudo /BiO/apps/perl-5.24.0/bin/perl -MCPAN "-e install 'DBD::SQLite'"

$ wget http://genetics.bwh.harvard.edu/pph2/dokuwiki/_media/polyphen-2.2.2r405c.tar.gz

$ tar xf polyphen-2.2.2r405c.tar.gz

$ cat >> ~/.bashrc

export PPH=/BiO/scratch/comteam/isbyeon/polyphen-2.2.2

export PATH="$PATH:$PPH/bin"

Ctrl+D

$ source ~/.bashrc

$ 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/

$ rsync -rltvz --delete-after rsync://rsync.cmbi.ru.nl/dssp/ $PPH/dssp/

$ cd $PPH/src

$ make download

$ make clean

$ make

$ make install

$ cd $PPH

$ ./configure

Example

$ cd $PPH

$ bin/run_pph.pl sets/test.input 1>test.pph.output 2>test.pph.log

$ bin/run_weka.pl test.pph.output >test.humdiv.output

$ bin/run_weka.pl -l models/HumVar.UniRef100.NBd.f11.model test.pph.output >test.humvar.output

$ diff test.humdiv.output sets/test.humdiv.output

$ diff test.humvar.output sets/test.humvar.output