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 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 but I have got some installation and usage issues, described here.

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.


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    $\begingroup$ 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! $\endgroup$ – terdon Jul 18 '18 at 17:10
  • $\begingroup$ I would like to do this analysis on a non-reference version of C. elegans. $\endgroup$ – charlesdarwin Jul 18 '18 at 18:11
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    $\begingroup$ 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? $\endgroup$ – terdon Jul 18 '18 at 18:48
  • $\begingroup$ @terdon I hope my question is clearer now. I have not tried BLAST. I am considering it. $\endgroup$ – charlesdarwin Jul 18 '18 at 21:11
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    $\begingroup$ @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! $\endgroup$ – Quantum7 Jul 30 '18 at 19:03

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