Proteomes from transcriptomic data

[qhelleu]

Hi,
Thanks for the very interesting soft/pipeline. I had a question regarding the input dataset. How does the program handles the presence of multiple isoforms (typical from transcriptomes) in the input proteome?
Thanks a lot.

[pskvins]

Hi,

Currently, we do not handle anything with isoforms,
so if multiple isoforms with similar sequences and lengths exist in the input proteome, unicore will consider those as multiple copies of genes instead of a single copy.
If the isoforms have big differences in sequence or length, unicore will capture those isoforms as different types of protein with a high chance, which will not be a problem when using unicore.

Our current recommendation on this problem is to select one isoform from multiple isoforms and make that the input proteome.

Please let us know if you have any further questions regarding it :)