SyMAP
Synteny Mapping and Analysis Program
Install / Use
/learn @csoderlund/SyMAPREADME
SyMAP (Synteny Mapping and Analysis Program)
Description: SyMAP is a software package for detecting, displaying, and querying syntenic relationships between a fully sequenced genome and (i) another sequenced genome, (ii) draft sequence, and (iii) self-synteny. It is designed for divergent eukaryotic genomes (not bacteria).
Download SyMAP tarball: https://github.com/csoderlund/SyMAP/releases. The SyMAP tarball contains the executable jar file, all necessary external software, and demo files.
Requirements: Java v17 or later and MySQL (or MariaDB). SyMAP uses MUMmer for the sequence to sequence alignment, which requires Perl. SyMAP has been tested on Linux and MacOS.
To use:
- Download the latest SyMAP tarball.
- Put the tarball in the location you want the symap_5 directory and untar it (tar xf symap_5.tar.gz).
- Follow the instructions in https://csoderlund.github.io/SyMAP/SystemGuide.html#demo to try the demo.
Full Documentation: https://csoderlund.github.io/SyMAP
SyMAP github code: To build, see SyMAP/java/README.
References:
C. Soderlund, M. Bomhoff, and W. Nelson (2011) SyMAP v3.4: a turnkey synteny system with application to plant genomes. Nucleic Acids Research 39(10):e68C. Link.
C. Soderlund, W. Nelson, A. Shoemaker and A. Paterson (2006) SyMAP: A system for discovering and viewing syntenic regions of FPC maps. Genome Research 16:1159-1168. Link.
