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Old 07-21-2016, 12:24 PM   #1
aprice67
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Question 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!
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Old 08-02-2016, 06:55 AM   #2
Melissa
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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.

https://genomevolution.org/coge/SynMap.pl
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