ConDo
Contact based protein Domain boundary prediction method
Pre-requisite:
PSIBLAST: ftp://ftp.ncbi.nlm.nih.gov/blast/executables/legacy.NOTSUPPORTED/2.2.26
! (is not blast+) ! 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
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
Installation:
git clone https://github.com/gicsaw/ConDo
cd ConDo
gcc src/feature.c -o bin/feature -lm -fopenmp -O2
or icc src/feature.c -o bin/feature -qopenmp -O2
Edit ConDodir variable in bin/ConDo.sh
Edit hhpath, condodir, database, and jackhmmerbin variables in bin/run_jackhmmer.sh
Edit blastbin, dbname, psipred, condodir, sann, NNDB_HOME variables in bin/gen_features.sh
Edit ccmpredbindir variables in bin/run_ccmpred.sh
Run examples:
We prepared two targets such as 1c7cA and 1sxjH in examples dir
!replace $target to 1c7cA or 1sxjH
cd examples/$target
Condo.sh $target.fasta $ncpu
Output file is $target.ConDo
First and second columns of the output file are residue index and domain boundary score, respectively
The cut-off of score is 1.4
In gnuplot, plot "$target.ComDo" u 1:2 w lp, 1.4
Etc:
bin/feature # generate input features of Machine learning and some other output files such as PAS, contact mat, modularity of contact.
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
References:
Hong, Seung Hwan, Keehyoung Joo, and Jooyoung Lee. "ConDo: Protein domain boundary prediction using coevolutionary information." Bioinformatics (2018).