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  • Identifying paralogs for a whole genome

    I have an e. coli genome and I want to know which genes are paralogs so I can investigate how RNA-seq reads are mapping to multiple positions. What I would like to do is get a full list of paralogs within my e.coli genome. I could blast the genome against itself and write some scripts to sort and select potential paralogs, but it seems like a problem that many people have likely encountered in the past and I don't want to reinvent the wheel if I don't have to. Is there a tool out there that can do this sort of thing already? Thanks very much!

  • #2
    SynMap seems to have E.coli genome. It will give you a dotplot and you can download the output files such as DAGchainer output files.

    The CoGe Comparative Genomics Platform. A software suite of interlinked and interconnected web-based tools for easily visualizing, comparing, and understanding the evolution, struture and dynamics of genomes.

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