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ConDo (Contact based Domain boundary prediction) was developed by Seung Hwan Hong
E-mail: [email protected]
version 0.5
paper: Protein Domain boundary prediction using Co-evolutionary information (in preparation for submission)
########## dependency ##############
PSIBLAST: (use not blast+)
ftp://ftp.ncbi.nlm.nih.gov/blast/executables/legacy.NOTSUPPORTED/2.2.26/
! with sqeucne database such as UniRef or NR
HHblitz:
https://github.com/soedinglab/hh-suite.git
PSIPRED:
http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/
SANN:
https://github.com/newtonjoo/sann
or https://lee.kias.re.kr
Jackhmmer:
http://hmmer.org/
! must install hmmer/easel (enclosed in hmmer)
! UniRef90 https://www.uniprot.org/downloads
! Use UniRef90 (recommended)
CCMPRED:
git clone --recursive https://github.com/soedinglab/CCMpred.git
python2
numpy
KERAS with TensorFlow or theano
gcc or icc
############################ generate features #########################
feature.c
compile:
gcc src/feature.c -o bin/feature -lm -fopenmp -O2
or icc src/feature.c -o bin/feature -qopenmp -O2
run: feature $target $Ncpu
Input files are:
$target.fasta # target sequence
$target.ss2 # Secondary Structure predicted by PSIPRED
$target.a22 # Solvent Accessibility predicted by SANN
$target.a3 # Solvent Accessibility predicted by SANN
$target.ck2 # sequence profile converted from chk of blast
$target.msa # multiple sequence alignment converted by Jackhammer
$target.ccmpred # predicted contact by CCMPRED
Outout files are
$target_feature.txt # input features for machine
$target_PAS3.txt # PAS information
result_ccm2.txt # predicted contact after filtering
community_ccm2.txt # Modularity of predicted contact
How to show
In gnuplot,
set size square
plot $target_PAS3.txt u 1:2:3, w image
plot result_ccm2.txt u 1:2:3, w image
plot community_ccm2.txt u 1:2 w lp
########################## How to run #########################
You need to set up the paths for programs and databases path of bash script (.sh) in bin directory
ConDo.sh
run_jackhmmer.sh
gen_features.sh
run_ccmpred.sh
run:
Condo.sh target.fasta $ncpu
Output file is $target.ConDo
First and second columns of the output file are residue index and domain boundary score, respectively
The cut-off of score is 1.2
In gnuplot,
plot "$target.ComDo" u 1:2 w lp, 1.2