Hi Anna, On Wed, 2015-12-16 at 11:04 +0100, Anna Schuster wrote:
> Hi there, > > I´m using the Mauve software and I have a short question. I´ve been > desperately searching the web for an answer but I can´t find it: > > I did a multiple alignment of 7 sequences and I´d be interested in > answering the following questions: > - how many locally collinear blocks (LCBs) were built in my alignment? In 2-way genome alignments there is a straightforward answer to this question, one simply counts the number of breakpoints. However for n-way genome alignments with n > 2 this quantity is not well-defined due to the existence of hidden breakpoints. You can read more about the issue in this publication by Kehr et al: http://arxiv.org/abs/1207.6964 When calculating the alignment, progressiveMauve uses pairwise LCBs to build up the multiple genome alignment. > - mean length of LCBs? see above. this quantity could only be calculated for pairwise projections, or on strictly core genome material (as in the original mauveAligner or via application of stripSubsetLCBs to a progressiveMauve alignment). > - shortest/longest block? same issues. > - multiple alignment of the 'core' region on average covered ...% ? This is a quantity you should be able to obtain with some simple processing of the .backbone file with your favorite program. Excel, LibreOffice, R, Python should all be able to easily parse the tab-delimited text file. > - nucleotide diversity (Π) for the concatenated aligned region > was ...? Mauve doesn't come with automated tools to calculate a quantity like this, but it would certainly be possible to cook something up with some basic scripting. > > 1. To answer those questions it´ll be important to see the "LCB > weight"-scale in the viewer. I downloaded a file from an online > publication (attachment 1), where they have that scale (upper corner > right). But I don´t find a way to show this feature in my own > alignment. Can you help me with that? Yes, that LCB weight slider will appear in pairwise alignments where the concept is well defined. > > 2. and where can I find the nucleotide diversity? > see above. likely to require some scripting, at the very least to concatenate alignment blocks into a single multi-fasta alignment for subsequent processing with another existing tool to calculate the quantity (assuming such a tool exists for standard multi-fasta alignments). 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.
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