Compressor of Multiple Sequence Alignments (CoMSA) is a tool to represent a family of aligned protein sequences (or a collection of families) in a highly compressed form. As an input it takes the FASTA (single aligned family) of Stockholm (collection of families) files. Pfam v. 31.0 Stockholm file of size 41.6 GB can be compressed to as 1.74 GB (compare to 5.6 GB for gzip). CoMSA is also significantly faster in compression than gzip. More details can be found in our paper pointed below.
CoMSA comes with a set of precompiled binaries for Windows and Linux. They can be found under Releases tab.
The software can be also built from the sources distributed as:
- Visual Studio 2017 solution for Windows,
- MAKE project (G++ 6.2 required) for Linux.
CoMSA can compress and decompress both FASTA files with aligned protein sequences as well as the protein families stored in Stockholm files (used in Pfam database).
CoMSA <mode> [options] <in_file> <out_file>
Parameters:
mode - Fc (Fasta compress), Fd (Fasta decompress), Sc (Stockholm compress), Sd (Stockholm decompress)
in_file - name of input file
out_file - name of output file
Options:
-w <width> - wrap sequences in FASTA file to given length (only for Fd mode); default: 0 (no wrapping)
-f - turn on fast variant (MTF in place of WFC)
Examples:
CoMSA Sc sample.stockholm sample.smsac
Compresses sample.stockholm file.
CoMSA Sc sample.stockholm.gz sample.smsac
Compresses sample.stockholm.gz file.
CoMSA Sd sample.smsac sample.stockholm.dec
Decompresses sample.stockholm file.
CoMSA Fc pf00005.26.fasta pf00005.26.msac
Compresses pf00005.26.fasta file.
CoMSA Fd -w 60 pf00005.26.msac pf00005.26.fasta.dec
Decompresses pf00005.26.fasta file and wrap the protein data to 60 columns.