Dear all,
please, may someone help me with any software or tool to detect repetitive regions within assembled bacterial genomes? preferred fit is a non-command line tool.
Thanks,
Hi Amro Hashish , I dont know of any ways to do this without a command line tool but I would say that using RepeatModeler from Repeatmasker: http://www.repeatmasker.org/ is quite straightforward to use and you will find many tutorials online to make a start (e.g. at http://www.repeatmasker.org/RepeatModeler/) . Otherwise I would look up any recent genome assembly paper but from what I have seen there is no standardised way of doing this and it depends on what you want to use the output for
Hi Amro Hashish. I think Repeatmasker Web Server (http://www.repeatmasker.org/cgi-bin/WEBRepeatMasker) is a good tool.
Hello Amro Hashish,
You can find repetitive elements using some software, which is Repeatmasker Web Server (http://www.repeatmasker.org/ ), Tandem repeat finder ( https://tandem.bu.edu/trf/trf.html), and Rapbase (using (https://www.girinst.org/repbase/ ). As well as, ıf you know to use, Geneious and DNAstar can help to answer your question like duplicate regions in the genome. Otherwise, this site also can help (http://dgd.genouest.org/ ).
Gözde Yildiz Rhewter Nunes
Thank you so much for letting me know.
these are working for all bacterial app?
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