Answers.Body: <p>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.</p>
  
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Answers.CreationDate: 2019-10-20T22:32:01.157Z
Answers.Text: can you give me example of ORF finder.
Answers.UserDisplayName: Ahmed M.Osman
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Answers.CreationDate: 2019-10-23T02:51:28.883Z
Answers.Text: 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.
Answers.UserDisplayName: Edward Kirton
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Answers.CreationDate: 2019-09-11T02:04:28.250Z
Answers.LastActivityDate: 2019-09-11T02:04:28.250Z
Answers.UserDisplayName: Edward Kirton
Body: <p>I have a protein Seq. and I want to know</p>
  
  <ul>
  <li>how to Know the longest ORF in this Protein?</li>
  </ul>
  
  <p>and if there is any tutorial for this process ?? </p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-09-09T17:14:34.547Z
Comments.Text: 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.
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-09-09T17:21:06.807Z
Comments.Text: 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.
Comments.UserDisplayName: terdon
Tags: <proteins><orf>
Title: how to Know the longest ORF in Protein?
ThreadText: # how to Know the longest ORF in Protein?
  
  (Asked by: username_0 on 2019-09-09)
  
  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 ??
  
  **Tags:** proteins, orf
  
  > **Comments:**
  > **username_1**: 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.  
  > **username_2**: 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.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_3 on 2019-09-11. Score: 2 | Accepted answer
  
  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.
  
  > **Comments:**
  > **username_0**: can you give me example of ORF finder.  
  > **username_3**: 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.  
  
  ---
  
  