Multi-way alignment and conservation
Marie-Laurence Cossette
I am trying to also run a mammalian alignment/conservation analysis but with a few other shrew species. My plan was to run Lastz for the new species against hg19 and then use the files from the ones you have online. I just have a few questions to make sure I am doing this correctly.
Were all the 93 hg19 chromosomes used (haplotypes, sex chromosomes, randoms etc..) against each species?
It’s mentioned that “Lineage-specific repeats were removed prior to alignment, then reinserted”. How was this done? Do you have a script for this part?
Thanks,
Marie
Gerardo Perez
Hello, Marie.
Thank you for your interest in the Genome Browser.
Our engineers have provided the following information:
Were all the 93 hg19 chromosomes used (haplotypes, sex chromosomes, randoms etc..) against each species?
Yes, all the sequences were used against each species.
It’s mentioned that “Lineage-specific repeats were removed prior to alignment, then reinserted”. How was this done? Do you have a script for this part?
Thank you for pointing out that the description page still says "Lineage-specific repeats were removed prior to alignment, then reinserted". While we did perform those extra steps many years ago for a small subset of mammalian species whose repeats had been categorized as "ancient" (predating the common ancestor) vs. "lineage-specific" (inserted after the common ancestor), in more recent times we no longer do that. We will update our description.
You may find our 470-way alignment track for hg38 on our development server helpful:
https://genome-test.gi.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&c=chrX&g=cons470way
It might have all the shrew species that you planned for mammalian alignment/conservation analysis. The track has not been reviewed by our Quality Assurance team, so we ask to exercise caution.
I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
Gerardo Perez
UCSC Genomics Institute
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