cross species multiple protein alignment
Kate Elliott
Hi,
I’ve been trawling your site (and other genome browsers) looking for pre-computed cross species protein alignments. I’m looking for the pileup of residues seen in a page such as this one:
However, I can’t find the source of the alignment in any of your downloads, but assume you must have it precomputed somewhere… Clicking on the alignment takes me to the nucleotide sequence which isn’t what I’m after. Do you know where I could obtain such an alignment? I want to use it to assess the level of conversation of an amino acid across as many species as possible as a way of prioritising nonsynonymous variants.
Any help gratefully received!
Kate
___________________________________
Dr Katherine Elliott
Senior Postdoctoral Bioinformatician
J Knight Group
Wellcome Trust Centre for Human Genetics
University of Oxford
Luvina Guruvadoo
http://hgdownload.soe.ucsc.edu/goldenPath/hg19/multiz100way/alignments/
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Kate Elliott
Hi,
In the process of parsing the knownCanonical.exonAA.fa.gz file, I’ve come across a couple of inconsistencies which have messed up my parser and don’t look like they are correct within the file.
The first 2 intervals I hit with this problem are:
>uc021ott.2_hg19_112_123 27 0 1 chr1:146446834-146446834+
LTDPCQPYRSAFYVLEQQRVGLAVDMD
(if it’s only 1 base wide, this interval shouldn’t be able to harbour this peptide)
and
>uc021ott.2_hg19_113_123 18 1 2 chr1:146446925-146447006+
EIEKYQEVEEDQDPSCPR
(again the size of the interval doesn’t fit the expected sized ORF of the peptide)
A look on the browser shows that for the first interval, there is a single base coding exon.
For the second interval, a look at the browser shows it containing the peptide for the first interval.
Something doesn’t seem right – is it me or is there an error??!!
Many thanks
Kate
Cath Tyner
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Cath Tyner
NEW: uc021ott.2_hg19_112_123 27 0 1 chr1:146446925-146447006 +LTDPCQPYRSAFYVLEQQRVGLAVDMD
OLD: uc021ott.2_hg19_112_123 27 0 1 chr1:146446834-146446834 +LTDPCQPYRSAFYVLEQQRVGLAVDMD
NEW: uc021ott.2_hg19_113_123 18 1 2 chr1:146447726-146447777 +EIEKYQEVEEDQDPSCPR
OLD: uc021ott.2_hg19_113_123 18 1 2 chr1:146446925-146447006 +EIEKYQEVEEDQDPSCPR
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Hello Kate,Thank you for providing these details; there was indeed a bug related to single base exons. This has been fixed, and downloads will be replaced soon - likely by next week. I will reply again when the downloads are available.
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