minmar/comer2 repository overview

COMER2, a cross-platform software package for protein remote homology search and alignment

(C)2013-2021 Mindaugas Margelevicius, Institute of Biotechnology, Vilnius University

⁠Description

The COMER method based on sequence profile-profile comparison is a sensitive, specific, and accurate computational tool developed for protein alignment and homology search. COMER version 2.2 (COMER2) represents one of the fastest implementations of calculations for sensitive protein homology search. High COMER2 performance is achieved by harnessing the power of the Graphics processing unit (GPU).

For details, please visit the github page at https://github.com/minmarg/comer2⁠

⁠Running a Docker container

The docker image encapsulates software dependencies. CUDA libraries, PSIPRED and BLAST software for incorporating secondary structure prediction into the profile using makepro.sh are included in the COMER2 docker image, so that the user can easily run COMER2 on GPU(s) without setting up CUDA drivers and installing external software before.

The user's system is supposed to be equipped with one or more GPUs with an installed NVIDIA graphics driver. There is no requirement for CUDA drivers to be installed. Yet, nvidia-docker2⁠ should be installed to enable the container to connect to the graphics driver. If the user's system already has a CUDA driver installed, it should be at least version 10.1 or upgraded otherwise.

The container for constructing a COMER2 profile can be used as follows. Let's assume that the user's directory ~/myhostdata contains an MSA myhostmsa.afa in aligned FASTA format. Then a profile can be constructed and written in the same directory (~/myhostdata/myhostmsa.pro) using the following command:

docker run --rm --name=comer2 --gpus=all --user="$(id -u):$(id -g)" -ti \
   -v ~/myhostdata:/myhome \
   minmar/comer2 \
   bin/makepro.sh -v -i /myhome/myhostmsa.afa -o /myhome/myhostmsa.pro

The first line specifies the container to be removed once finished execution (the image is not removed). The host directory ~/myhostdata is mounted on the container's directory /myhome for data exchange in the second line (access from within the container to the host system is not possible). The third line specifies the image name, and the fourth line corresponds to the container's command with its arguments (makepro.sh in this case).

COMER2 search is initiated similarly:

docker run --rm --name=comer2 --gpus=all --user="$(id -u):$(id -g)" -ti \
   -v ~/myhostdata:/myhome \
   -v /data/databases/profile_dbs:/mydb \
   minmar/comer2 \
   bin/comer -v -i /myhome/myhostmsa.pro -d /mydb/pdb70_210331 -o /myhome/comer_output

The main difference from the preceding command is the third line, which mounts the directory of profile databases /data/databases/profile_dbs in the host system on the container's directory /mydb.