Question: Ultra-Conservation In Genome Comparisons
gravatar for Haibao Tang
9.1 years ago by
Haibao Tang3.0k
Mountain View, CA
Haibao Tang3.0k wrote:

Part of my research interest is to look for unusual conservation patterns in pairwise genome comparisons. Naturally, such patterns might suggest functional elements, or occasionally, lateral DNA transmission between organisms.

I have so far relied on ad-hoc rules to extract these. However, the same rule does not apply to a different species pair - for example, some would find a 200bp perfect match between chicken-human unusual, but it is a lot less surprising for chimp-human comparison.

My question here is whether there is a statistical method to measure the "surprise" of an alignment, given the expected sequence divergence between two species? I realize there could be complications as selective pressure varies for different types of sequences - but would like to see what others approach this problem.

ADD COMMENTlink written 9.1 years ago by Haibao Tang3.0k
gravatar for Khader Shameer
9.1 years ago by
Manhattan, NY
Khader Shameer18k wrote:

Have you looked at the extensive genome comparison studies reported by Inna Dubchuk's group?

I would recommend you to start with the manuscripts that described genome comparison based on multiple alignments and pairwise alignments from the group (dataset, methods). Pre-computed data and an associated comparative genome browser Vista could be useful for you.

ADD COMMENTlink modified 11 months ago by RamRS23k • written 9.1 years ago by Khader Shameer18k
gravatar for Aaron Statham
9.1 years ago by
Aaron Statham1.1k
Aaron Statham1.1k wrote: and may be useful background

ADD COMMENTlink written 9.1 years ago by Aaron Statham1.1k

thanks for the pointer. According to the paper, "We identify HCNEs by scanning pairwise BLASTZ net whole-genome alignments (nets) downloaded from the UCSC Genome Browser database for regions with at least I identities over C alignment columns." - this is an arbitrary rule that I mentioned, which I hope that there is a better alternative to.

ADD REPLYlink written 9.1 years ago by Haibao Tang3.0k
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