“synteny.py assemble” obtain too many gene pairs.

[ZhaoHang-bio]

Hi，Prof. Haibao Tang.

Thank you for developing the very useful software 'synteny.py assemble', which allows me to draw microsynteny graphs based on multiple sequences. However, I have observed that the threshold for calculating homologous genes in this command seems to be too low, and the number of gene pairs obtained by 'catalog.py ortholog' and 'synteny.py mcscan' is much lower than the number obtained by 'synteny.py assemble'. Do you have any solutions to this issue?

[tanghaibao]

@ZhaoHang-bio

Unfortunately synteny assemble is meant to be a more sensitive method. This is useful only when the regions are known to be syntenic and a gene pair will be reported as long as there is a LAST match.

If you are concerned about the increased sensitivity, then using the gene pairs in the traditional way (catalog ortholog or synteny mcscan) may be desirable since they filter BLAST results more aggressively.