Perl Script To Retrieve All Orf?

Question

[Adrian Pelin]

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

[Michael]

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

[Adrian Pelin]

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.

[Michael]

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

[Abhishek]

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

Answer 1

[Rahul Sharma]

Hi

From EMBOSS toolkit:

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

Cheers!