Perl Script To Retrieve All Orf?
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10.5 years ago
Adrian Pelin ★ 2.6k

Hello,

I have a draft assembly. Does anyone know of scripts to retrieve all ORF in protein format from a a fasta file of contigs?

Adrian

orf perl • 4.3k views
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Unless this is a prokaryote, getting all open reading frames from a draft assembly is not an informative analysis (splicing, low gene density), and also for bacteria it is of very limited use. Instead, look for gene prediction , e.g. on BioStar: gene-prediction

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I work on microsporidia. They have very little introns (up to 20 genes with introns, some none at all) and small genomes. They are Eukaryotes.

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Then you can use getorf as suggested by R@hul, you should still attempt to do a proper gene prediction.

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Please share the fully functional perl script to translate CDNA to ORF (protein) selecting the longest one only. I have Active Perl installed.

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10.5 years ago
Rahul Sharma ▴ 660

Hi

From EMBOSS toolkit:

getorf -sequence genome.fasta -outseq genome.ORFs -minsize 180 -find 1 &

Cheers!

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