I could swear that when I used mummer(nucmer) in the past, with the default -mum option, it would not find any hits off of the main diagonal, for the simple reason that there can be no unique seeds off of the main diagonal. However now I am seeing that off-diagonal hits are found. I'm not sure what version of mummer I'm using, unfortunately…but is this possible?
By default, mummer now runs in "-mumreference" mode, which only forces matches to be unique in the reference (and not necessarily the query). That may be contributing to what you see. You can switch back to full uniqueness with the -mum option. Also, if the "off diagonal" hits show up in mummerplot as blue, they are reverse complement hits, which often appear off diagonal.
Ah, yes I think they are reverse complement hits! Thank you. But I think for a self-alignment the first issue, regarding mumreference, is not relevant is it? Because if reference and query are the same, then uniqueness in query is the same as uniqueness overall.
That's right. When aligning something against itself, mum or mumref shouldn't make a difference.
You undoubtedly ensure it is appear simple along with your business presentation nonetheless i come across this kind of subject being truly an issue that I believe I may never recognize. It appears also complex and really wide personally. I will probably be impatient for your next article, I am going to try to get the hang of it!
ugg australia http://www.snowbootser.com
Hey really nice blog!! Man .. Beautiful .. Incredible .. I will bookmark your web site and take the feeds alsoI'm satisfied to seek out numerous helpful info here within the post, we need to have develop much more techniques on this regard, thanks for sharing.
After research just a few of the weblog posts on your website now, and I truly like your method of blogging. I bookmarked it to my bookmark website list and can be checking again soon. Pls take a look at my website as properly and let me know what you feel.
moncler italy sale http://www.monclereu.it
Log in to post a comment.