forked from searphsea/COLORS
-
Notifications
You must be signed in to change notification settings - Fork 0
Protein contacts prediction
License
SSchott/COLORS
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Folders and files
Name | Name | Last commit message | Last commit date | |
---|---|---|---|---|
Repository files navigation
<1>Installation step1: Install Eigen, a C++ library for calculating SVD. Eigen can be download from https://bitbucket.org/eigen/eigen/get/3.2.6.tar.bz2 step2: Complie COLORS using the following command: g++ -o colors main.cpp colors.h colors.cpp matrix.h matrix.cpp sequence.h sequence.cpp type.h -O3 -Iyour_eigen_install_dir/include/eigen Please replace your_eigen_insall_dir with the directory you specificed in step1. <2>Usage ./colors msa-file output-prefix The MSA is represented by a M by N matrix, where M is the number of sequences and N is the length of the target. COLORS will output 6 files: output-prefix.mi_lrs, output-prefix.omes_lrs, output-prefix.cov_lrs, output-prefix.mi_score, output-prefix.omes_score and output-prefix.cov_score. output-prefix.mi_lrs is the sparse matrix calculated by COLORS given the original MI matrix. output-prefix.mi_score has 5 columns: position_i, position_j, original_score, apc_score and lrs_score. <3>Contact and Citation Haicang Zhang, Yujuan Gao, Minghua Deng, Chao Wang, Jianwei Zhu, Shuai Cheng Li, Wei-Mou Zheng, Dongbo Bu. Improving residue–residue contact prediction via low-rank and sparse decomposition of residue correlation matrix. Biochemical and biophysical research communications 472.1 (2016): 217-222.
About
Protein contacts prediction
Resources
License
Stars
Watchers
Forks
Releases
No releases published
Packages 0
No packages published
Languages
- C++ 98.5%
- Makefile 1.5%