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 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.