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wyp1125 / MCScanX

MCScanX: Multiple Collinearity Scan toolkit X version. The most popular synteny analysis tool in the world!
http://chibba.pgml.uga.edu/mcscan2/
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Format of xyz.homology? #59

Open scottcain opened 1 year ago

scottcain commented 1 year ago

In the readme, there is this section:

[MCScanX_h](https://github.com/wyp1125/MCScanX#id8)

The BLASTP input of MCScanX can be replaced by a tab-delimited file containing more reliable pairwise
homologous relationships. In this case, users should use MCScanX_h instead. The executation of 
MCScanX_h is very similar to that of MCScanX, except that the "xyz.blast" file should be replaced by 
"xyz.homology" file. At the bottom of screen output, statistics on numbers / percentages of collinear 
homolog pairs are shown.

But says nothing about how this homology file should be formated. Can you please define this better, perhaps with an example?

gunjanpandey commented 1 year ago

@scottcain - Have you worked out the format of "xyz.homology"? If so, could you please explain?

SalvadorGJ commented 1 day ago

Any news about this issue?

scottcain commented 1 day ago

So I don't know for sure what the (right) answer is, but for my own usage, I created a three column tab delimited file, with column 1 being the protein id from species 1, likewise for column 2 and then a score in column 3, which in practice was "100" since I was usually pulling these homology/orthology relationships from MODs where the relationships are human curated.