Include STOP codon in getorf output
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2.7 years ago
lokdeep17 • 0

I am using getorf from EMBOSS. I want to include the STOP codon in my output file in the nucleotide format. But no matter what I try, the output is without STOP codon. Any suggestions? Example: My input file (named as input.fa) is:

>a
TAGATCCTTTCTTTCTTGTCTCTATATTACAAGGGAGTACAAAAAAGGATTATGAATATATGAAAAGAAAATTTTGAAGATAAATAAAACGGCAATTTACGTACCTAGAACAATGGCAGGACGTACTCAGGCCCTGTCCCAATCAAACATGCCATGCACATACATCTATTCTTGAAATCTCAAGGGAGACTATTTTCTAAAAAGCACCAGATTTTTTCAATTGAACATAACAGGCAACAAATGGAATAGCAAATCCAACAGCGAAGAACCCAAAATGAGAAAGAGCATAGGGCGTCTTTCTACCTTTGACTTTGAATGGAATATTCTCATACACACCATCTTTGAAATGGACTGATCTCTTCATGATAATTGGTCTAGCCATAATATTGCTACTTCTCTTTGCTGCGGTTCTAATCATTTGTTGGCACAACATTGTGTATTGAGTATGACTTCTTCTCTATTTAATTGATATGTTGTATGCTTTCTTGAAATCAGTAGACTATAAGATCGTTCTTGTAAATCATTAATCTAACCTTATGAGTTATGCTGTGGTCAATCTTTATTTTCTGTTTTTCTTGATCCCCTAGCTCTTCCGTAAACACCGAACACTTTCTCTCACATGATTGGTGCAAA


output file looks like (named as longest.fa) :

>a_3 [433 - 200] (REVERSE SENSE)
ATGTTGTGCCAACAAATGATTAGAACCGCAGCAAAGAGAAGTAGCAATATTATGGCTAGA
CCAATTATCATGAAGAGATCAGTCCATTTCAAAGATGGTGTGTATGAGAATATTCCATTC
AAAGTCAAAGGTAGAAAGACGCCCTATGCTCTTTCTCATTTTGGGTTCTTCGCTGTTGGA
TTTGCTATTCCATTTGTTGCCTGTTATGTTCAATTGAAAAAATCTGGTGCTTTT


as you can see, this does not have a stop codon in the end. the command that I used is: hmmer2go getorf -i input.fa -o longest.fa -t3 I want stop codon to be included.

emboss getorf orf STOP • 935 views
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hmmer2go getorf --man


Does it have such option?

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I couldn't either. Weird they didn't give the option

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I doubt many people use it for protein prediction these days..

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If there's some other ORF finder to do this job, please suggest it to me.

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I haven't done this for quite a few years, but back then I swore by https://github.com/hyattpd/Prodigal

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are you looking for true ORFs as in genes or simply ORFs between two stopcodons?

Perhaps get_longest_orf, TransDecoder, FrameD, ... can be of use (most will look for true genes though)

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I tried get_longest_orf.pl, it also does not include STOP codon in the output.

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you are correct. and as it turns out it itself is based on EMBOSS so to be expected behavior (and thus my bad to list that one)

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Prodigal is a great tool but for microbes.

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Why do you think it's just for microbes?

-g:  Specify a translation table to use (default 11).

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It's not just the translation table, it's identifying TSS and other stuff. Take a look at the paper