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How does nanopore allow targeted sequencing of large genomic regions? JackieBadger General 10 02-28-2014 05:20 PM
Finding common genomic regions... milesgr Bioinformatics 0 03-27-2013 06:54 AM
Determine conservation levels across species cmnailecin Bioinformatics 0 02-24-2013 05:12 PM
extracting conservation scores for large sets of genomic regions dphansti Bioinformatics 0 01-11-2013 06:19 PM

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Old 07-05-2014, 01:46 AM   #1
emanlee
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Smile Is there a way to determine the conservation of any genomic regions?

We identified a long intergenic non-coding RNA in chicken, for example, located:
exon1, chr1, 200000,201000,+
exon2, chr1, 203000,204000,+
Is there a way to determine conservation levels across species? Thanks!
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Old 07-05-2014, 05:50 AM   #2
GenoMax
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You can find pre-computed pair-wise alignments and multiple alignments for the chicken genome here: http://hgdownload.soe.ucsc.edu/downloads.html#chicken

Resources at Ensembl: http://www.ensembl.org/info/genome/compara/index.html
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Old 07-05-2014, 10:50 AM   #3
biocomputer
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On the UCSC Genome Browser, version WUGSC 2.1/galGal3 of the chicken genome has several conservation and comparative genomics tracks but this version is from 2006. The newer version ICGSC Gallus_gallus-4.0/galGal4 doesn't seem to have that many related tracks. I think these tracks are basically showing the data that GenoMax linked to but they're already in genome browser form.
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Old 07-05-2014, 07:16 PM   #4
emanlee
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Thanks. For the well-studied organisms, there are multiple alignments. We can get phastcons and take them as conservation levels. For others, such as Alpaca genome, there are only pairwise alignments and no pre-computed phastcons, how to get conservation levels? Thanks again!
Can we indirectly get the phastcons? For example, what we want is to get the conservation levels of 'Alpaca, chr1, +, 2000,000--2000,006'.
First, we get the corresponding positions/regions on human genome, say 'Human, chr1, +, 2100,000--2100,006', according to the pairwise alignment Alpaca/Human. (http://hgdownload.soe.ucsc.edu/golde...icPac2/vsHg19/)
Then, we get the phastcons of 'Human, chr1, +, 2100,000--2100,006' according to human 100-way multiple alignment (http://hgdownload.soe.ucsc.edu/golde.../multiz100way/).

Last edited by emanlee; 07-05-2014 at 08:02 PM.
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