0
$\begingroup$

I have a protein Seq. and I want to know

  • how to Know the longest ORF in this Protein?

and if there is any tutorial for this process ??

$\endgroup$
2
  • 1
    $\begingroup$ Hi, you need to supply example data. The question has been asked and answered several times already and referring to past posts would help get you started. $\endgroup$ – M__ Sep 9 '19 at 17:14
  • 5
    $\begingroup$ If you have a protein sequence, you already have the ORF. I assume you mean you have a DNA sequence, not a protein sequence, right? In what species? Is there splicing? Is this a bacterium or a eukaryote? Please edit your question and give us some context. Add the actual sequence and the organism. $\endgroup$ – terdon Sep 9 '19 at 17:21
2
$\begingroup$

Proteins don't have ORFs, DNA sequences do. What DNA sequences do you have? If cDNA (i.e. transcript/mRNA) then an ORF finder will give multiple ORFs and the coordinates on the full-length input DNA which indicate it's length.

$\endgroup$
2
  • $\begingroup$ can you give me example of ORF finder. $\endgroup$ – Ahmed M.Osman Oct 20 '19 at 22:32
  • $\begingroup$ EMBOSS has ORF finder, but it will find all ORFs, which may not be what you want (e.g. you may have to post-process to pick the longest of the overlapping ORFs). Usually folks use a gene-finder instead, which includes an ORF finder but also other features, such as promoter/transcriptional start site and may include special handling for intron/exon boundaries (i.e. for eukaryotes). I like Prodigal for microbiome data but there are several choices including genemark, fgenesh, glimmer/glimmerhmm, genscan although particular genefinders are usually suited for either prokaryotes or eukaryotes. $\endgroup$ – Edward Kirton Oct 23 '19 at 2:51

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.