Hi Manal, On Wed, 2014-05-28 at 23:45 +1000, Manal Farid wrote: > this is very useful but why when blast one of the unordered contigs it > shows 100% similarity to the reference (but it was not aligned > properly by Mauve.
this happens frequently when the contig has sequence for a multi-copy gene family (e.g. transposase, transporter, some others). The positionally-conserved copy of the gene will get aligned, but additional copies present in the assembly will not become aligned. There may be other reasons such a scenario could arise but the multi-copy gene family situation is most likely. > > Also, can see a contig at the middle of the graph that has no > similarity to the reference strain (not at the right side_- is this > possible? Possibly there is a small region on one end of the contig that did align? I don't think the contig mover places a constraint on the minimum fraction of the contig that must align in order for the contig to be placed. Best, -Aaron -- 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. ------------------------------------------------------------------------------ Time is money. Stop wasting it! Get your web API in 5 minutes. www.restlet.com/download http://p.sf.net/sfu/restlet _______________________________________________ Mauve-users mailing list Mauve-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mauve-users
