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 ??
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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, 2019 at 17:14
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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. $\endgroup$– terdonSep 9, 2019 at 17:21
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1 Answer
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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.
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$\begingroup$ can you give me example of ORF finder. $\endgroup$ Oct 20, 2019 at 22:32
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$\begingroup$ 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. $\endgroup$ Oct 23, 2019 at 2:51