Hi Evan, On Wed, 2010-11-24 at 13:42 -0500, Snitkin, Evan (NIH/NHGRI) [F] wrote: > Hello, > > I have an extremely mundane question. I am using the ortholog exporter and > would like some additional flexibility in the alignment coverage threshold. > Right now it is required that the coverage be between 51% and 100%. In > practice, this means that the lowest allowed value is 52%. Is it possible to > lower it slightly? Specifically, I would love it if it was greater than or > equal to 50%.
The restriction that orthologs (actually they should really be called "positional homologs") must overlap by at least 50% had been put in place because if features with less overlap are permitted to cluster then it becomes possible for a group of homologs to grow along a sequence to include a large number of features that may not overlap at all. In practice this might happen only very rarely, so I've committed a change to the source code that relaxes the strict requirement that homologs overlap in at least 50% of their length. Any minimum threshold can now be specified, but thresholds below 50% will produce a warning message. On a related note, Martin Wu, Meg Woolfit and others have pointed out that sometimes problems exist with the alignments exported by the ortholog export tool. Occasionally some of the alignments were reversed, but not complemented. Please accept my apologies if this bug has affected your work. It's now fixed and the fix will appear in all forthcoming auto-generated Mauve snapshot releases. Please note that this is not a problem with progressiveMauve or mauveAligner-generated XMFA alignments, it is only the alignment file generated by the "Export orthologs" menu option that is affected. Regards, -Aaron ------------------------------------------------------------------------------ Increase Visibility of Your 3D Game App & Earn a Chance To Win $500! Tap into the largest installed PC base & get more eyes on your game by optimizing for Intel(R) Graphics Technology. Get started today with the Intel(R) Software Partner Program. Five $500 cash prizes are up for grabs. http://p.sf.net/sfu/intelisp-dev2dev _______________________________________________ Mauve-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/mauve-users
