Syntenic regions and homologous genes identification with SynMap (CoGe) workflow

SynMap

Generates a syntenic dotplot between two organisms and identifies syntenic regions. SynMap is a web-based tool which allows researchers to explore whole genome synteny patterns across two genomes. The software finds putative genes or regions of homology between two genomes, identifies collinear sets of genes or regions of sequence similarity to infer synteny and generates a dotplot of the results and coloring syntenic pairs. [source : omictools]

More informations : https://genomevolution.org/wiki/index.php/SynMap

SynMap Methods :

1. Extract sequences for comparison; build fasta files
2. Create blastable databases (if necessary) and compare using
   1. Last, a variant of Blast, much faster than lastz, nearly as sensitive. Last Homepage: http://last.cbrc.jp/
   2. lastz, a variant of blastz 
   3. MegaBlast
   4. Discontinuous MegaBlast
   5. TblastX
   6. BlastP
   7. BlastN. SynMap uses default blast parameters with an e-value cutoff of 0.001.
3. Identifies tandem gene duplicates using a program written by Haibao Tang and Brent Pedersen called blast2raw. Tandem gene duplicates are then condensed and treated as a single gene. These can later be output and downloaded in a file to be investigated further.
4. Filters repetitive matches, e.g. high copy number genes, using a program written for SynMap by Brent Pedersen
5. Identify syntenic pairs of by finding collinear series of putative homologous sequences using DAGChainer 

Sources (scripts) : https://github.com/LyonsLab/coge/tree/master/scripts/synmap