SyMAP Docs

SyMAP Documentation Pages

Documentation

Main page
Input and xToSymap
- NCBI to SyMAP input
- Ensembl to SyMAP input
System Guide (symap)
User Guide (symap or viewSymap)
- Queries
- Details - collinear sets, conserved genes, hits.
Tour
Release Notes

Publications

All upgrades since 7-Nov-2016 (pre-v5) have been developed by CAS without funding or updated publication.

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):e68 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

SyMAP uses MUMmer^1,2 for computing the alignment between two genomes.

History of SyMAP

FPC (FingerPrinted Contig, Soderlund et al. (2000) Genome Research) was written to build physical maps from fingerprinted clones, but is obsolete now. SyMAP was originally written for FPC maps-to-sequence synteny (FPC User Guide), then was upgraded for sequence-to-sequence synteny. FPC was removed from SyMAP in v5.0.8, but is still available from Github downloads and www.agcol.arizona.edu.

Email Comments To: symap@agcol.arizona.edu