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bioinfologics / satsuma2

FFT cross-correlation based synteny aligner, (re)designed to make full use of parallel computing
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homologous comparison #17

Closed mictadlo closed 4 years ago

mictadlo commented 5 years ago

Hi, I ran satsuma with default settings to do a homologous comparison. Looking at MizBee output each chromosome match to its own. I would have expected to see that they would be other relationships between the chromosomes. Or do I have to use different settings for homologous comparison?

Thank you in advance,

Michal

jonwright99 commented 5 years ago

Hi Michal,

Satsuma is designed to find the single best match so comparing all-to-all will only find the matching chromosome. One way to find the best secondary matches would be to compare each chromosome to all the others except itself, however this would not find any additional matches (third best etc.). Satsuam2 is not really designed for this type of comparison out of the box and there are probably better tools to use, eg. orthoMCL for gene-based comparisons.

Best, Jon