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  • 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!

  • #2
    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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    • #3
      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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      • #4
        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, 07:02 PM.

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