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hyattpd / Prodigal

Prodigal Gene Prediction Software
GNU General Public License v3.0
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Parameter of lenght of ORFS #69

Open mattoslmp opened 4 years ago

mattoslmp commented 4 years ago

How Can I change the length parameter of predicted ORFs. I would like to specify sequences > 15bp, predict sequences larger than this size.

tseemann commented 4 years ago

Prodigal doesn't predict ORFs - it finds genes (which are substrings of ORFs). If you want ORFs, try orfm.

It is not possible to change the MIN_GENE size via the command line. You need to edit the source code and recompile.

But 15bp is far too small, you will get 1000s of false positives. There are very few real genes that small. You could build a DB of the tiny ones and then tblastn them to assign them.

mattoslmp commented 4 years ago

Thank you for your help and explanation @tseemann.

KeyLllll commented 9 months ago

@tseemann Hi！I would like to predict genes between 33 and 303 bp. How can I edit the source code and recompile? Thanks！

ZhangDengwei commented 1 month ago

@KeyLllll Have you solved this issue?