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EddyRivasLab / hmmer

HMMER: biological sequence analysis using profile HMMs
http://hmmer.org
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select suitable sequence length #297

Closed AlisaGU closed 1 year ago

AlisaGU commented 1 year ago

Hi, following your advice, I got ORFs instead of the translated genome via breaking the translated genome by stop codons. A lot of ORFs are shorter than 5bp, and it seems that it's too short to predict by hmmer3. Filtering is a good solution to avoid this problem. Could you give me some tips about a suitable sequence length threshold to filter?

cryptogenomicon commented 1 year ago

That's something you have to decide. It's not really a problem for HMMER if you have short ORFs (even 1 aa); you just won't tend to be able to find significant matches to very short ORFs.