Body: <p>Are there any tools for finding duplications from a whole genome in FASTA format?</p>
  
  <p>Let's say the genome has gene A duplicated somewhere in the genome and gene B triplicated in tandem elsewhere in the genome. Is there a tool that will output a list of gene A and gene B with location and number of copies?</p>
  
  <p>I am currently using <a href="http://www.ruhr-uni-bochum.de/ecoevo/cm/cm_phobos.htm" rel="nofollow noreferrer">phobos</a> to annotate tandem repeats in the genome of <em>C. elegans</em> but it becomes very slow beyond repeats of 100 bp. Does anybody know of a tool for gene-size/larger repeats?</p>
  
  <p>I have tried to use <a href="https://github.com/acg-team/tral" rel="nofollow noreferrer">TRAL</a> but I have got some installation and usage issues, described <a href="https://github.com/acg-team/tral/issues/12" rel="nofollow noreferrer">here</a>.</p>
  
  <p>I cannot use the annotation because I would like to apply this tool to a non-reference version of a <em>C. elegans</em> genome, for which no annotation is available.</p>
  
  <p>Specifically, I would like to annotate the Hawaiian strain, which is a strain very divergent to the reference N2 strain. I am not looking into particular genes, just natural genetic variation.</p>
  
  <p>I have not tried BLAST. It would be a possibility but I wonder if there are others.</p>
  
  <p>Cheers.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-07-18T17:10:34.343Z
Comments.Text: If you're working on _C. elegans_ isn't this information already available? Surely the duplicated genes will be well known in an organism this well studied!
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-07-18T18:11:19.123Z
Comments.Text: I would like to do this analysis on a non-reference version of C. elegans.
Comments.UserDisplayName: Biomagician
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-07-18T18:48:18.017Z
Comments.Text: Please [edit] your question and explain more clearly. If this is for a *C. elegans* genome, why would you expect it to be significantly different? Can you at least assume it will be similar enough that you will have a known set of genes to look for? Do you only want to look for gene duplications or large repeats in general? Have you tried simply blasting (tBLASTn) all known C. elegans proteins against the genome?
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-07-18T21:11:53.340Z
Comments.Text: @terdon I hope my question is clearer now. I have not tried BLAST. I am considering it.
Comments.UserDisplayName: Biomagician
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-07-30T18:58:17.860Z
Comments.Text: @terdon The orthologs will be annotated for *C. elegans* (e.g. OMA, OrthoDB, etc), but the number or tandem repeats likely will not be annotated.
Comments.UserDisplayName: Quantum7
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-07-30T19:03:08.383Z
Comments.Text: @charlesdarwin I'm not aware of any tools that output both number of repeats and homology information. That would be a useful DB. I'm hoping someone answers this in the affirmative!
Comments.UserDisplayName: Quantum7
Tags: <software-recommendation><sequence-annotation><cnv><repeat-elements>
Title: Detect gene duplication events from a whole genome in FASTA format
ThreadText: # Detect gene duplication events from a whole genome in FASTA format
  
  (Asked by: username_0 on 2018-07-18)
  
  Are there any tools for finding duplications from a whole genome in FASTA format?
  
  Let's say the genome has gene A duplicated somewhere in the genome and gene B triplicated in tandem elsewhere in the genome. Is there a tool that will output a list of gene A and gene B with location and number of copies?
  
  I am currently using [phobos](http://www.ruhr-uni-bochum.de/ecoevo/cm/cm_phobos.htm) to annotate tandem repeats in the genome of *C. elegans* but it becomes very slow beyond repeats of 100 bp. Does anybody know of a tool for gene-size/larger repeats?
  
  I have tried to use [TRAL](https://github.com/acg-team/tral) but I have got some installation and usage issues, described [here](https://github.com/acg-team/tral/issues/12).
  
  I cannot use the annotation because I would like to apply this tool to a non-reference version of a *C. elegans* genome, for which no annotation is available.
  
  Specifically, I would like to annotate the Hawaiian strain, which is a strain very divergent to the reference N2 strain. I am not looking into particular genes, just natural genetic variation.
  
  I have not tried BLAST. It would be a possibility but I wonder if there are others.
  
  Cheers.
  
  **Tags:** software-recommendation, sequence-annotation, cnv, repeat-elements
  
  > **Comments:**
  > **username_1**: If you're working on _C. elegans_ isn't this information already available? Surely the duplicated genes will be well known in an organism this well studied!  
  > **username_0**: I would like to do this analysis on a non-reference version of C. elegans.  
  > **username_1**: Please [edit] your question and explain more clearly. If this is for a *C. elegans* genome, why would you expect it to be significantly different? Can you at least assume it will be similar enough that you will have a known set of genes to look for? Do you only want to look for gene duplications or large repeats in general? Have you tried simply blasting (tBLASTn) all known C. elegans proteins against the genome?  
  > **username_0**: @username_1 I hope my question is clearer now. I have not tried BLAST. I am considering it.  
  > **username_2**: @username_1 The orthologs will be annotated for *C. elegans* (e.g. OMA, OrthoDB, etc), but the number or tandem repeats likely will not be annotated.  
  > **username_2**: @charlesdarwin I'm not aware of any tools that output both number of repeats and homology information. That would be a useful DB. I'm hoping someone answers this in the affirmative!  
  
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  ## 0 answers
  
  