Re: [Mauve-users] Mauve statistics
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koadman
From: Aaron D. <aar...@ut...> - 2017-02-08 20:39:15
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Hello Mathias, The information you are asking for exists in the XMFA file, and in fact if you just delete the sequences from the XMFA file the representation of that information becomes fairly succinct. Maybe a clever series of grep commands could get you there, or some regular expressions. I guess you are seeking this information in a tab delemited format? There are no programs bundled with Mauve that would produce the info in a such a format. The closest would probably be the .bbcols and .backbone files, but those also break up the blocks at the boundaries of gain & loss events that are longer than around 20nt, so probably wouldn't be quite what you want for your score idea. Not sure if its helpful for your goals, but Mauve has a few rearrangment distances implemented in the GUI, including double-cut join and single-cut join, and breakpoint counts themselves have been used as a statistic for genome rearrangement. These distances can only be defined on genome alignments that have equal gene content in all genomes, which isn't usually the case with progressiveMauve unless the subset LCBs have been stripped out, or just 2 genomes were aligned. Best, -Aaron On Wed, 2017-02-08 at 06:51 -0500, Mathias Lorieux (GMail box) wrote: > Hi all, > > I’d be grateful if I could get help on how to obtain summary > statistics on alignments that Mauve produces. > > What I am looking for is a summary of the rank position, size, start- > stop of each ’block’ that Mauve identifies, for each compared > sequence. > > From these statistics I aim to calculate a kind of re-shuffling score > between two sequences. > > Thanks very much, > Mathias > > > ------------------------------------------------------------------- > ----------- > Check out the vibrant tech community on one of the world's most > engaging tech sites, SlashDot.org! http://sdm.link/slashdot > _______________________________________________ > Mauve-users mailing list > Mau...@li... > https://lists.sourceforge.net/lists/listinfo/mauve-users -- Aaron E. Darling, Ph.D. Associate Professor, ithree institute University of Technology Sydney Australia http://darlinglab.org twitter: @koadman UTS CRICOS Provider Code: 00099F DISCLAIMER: This email message and any accompanying attachments may contain confidential information. If you are not the intended recipient, do not read, use, disseminate, distribute or copy this message or attachments. If you have received this message in error, please notify the sender immediately and delete this message. Any views expressed in this message are those of the individual sender, except where the sender expressly, and with authority, states them to be the views of the University of Technology Sydney. Before opening any attachments, please check them for viruses and defects. Think. Green. Do. Please consider the environment before printing this email. |