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Old 11-30-2015, 08:01 AM   #1
antifolate
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Default Need suggestions to quantify genomic activity

Hello,

I'm trying to compare different strands of s.pombe, primarily in terms of genomic activity. What I mean by that is insertions, deletions, and rearrangements. I'm still looking for a good way to quantify genomic activity, especially rearrangements. Is there a standard way to do this?

By looking at Mauve's output, it seems that the number of contigs with breakpoint (contigs with more than one color) could be a good quantifier, if normalized by the number of overall mapped contigs for example. However, there's no way to automate the extraction of these kinds of contigs, so I'd have to count them by hand.

I've been looking for papers who might have done something similar but couldn't really find anything useful. Please let me know if you have an idea.

Thanks.
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Old 11-30-2015, 08:13 AM   #2
GenoMax
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Have you seen this paper: http://gbe.oxfordjournals.org/content/6/9/2557.full

Last edited by GenoMax; 11-30-2015 at 08:43 AM.
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Old 11-30-2015, 08:40 AM   #3
antifolate
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Thanks @GenoMax. This paper is rich in information and I've already learned several things. But the authors don't seem to have studied rearrangements (?) which I'm interested in.
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