Hi Bron,<div><br></div><div>The sentence "<span style>but it's a string of 1000 Ns (Pseudoautosomal region)" does not make sense to me. First, the region is 10000, not 1000 bp long, second, this is not a pseudo autosomal region, but the regions that are identical to X are.</span></div>
<div><font color="#222222" face="arial, sans-serif"><br></font></div><div><font color="#222222" face="arial, sans-serif">Cheers,</font></div><div><font color="#222222" face="arial, sans-serif">Bert<br></font><br><div class="gmail_quote">
On Mon, Jun 11, 2012 at 1:35 PM, Bronwen Aken <span dir="ltr"><<a href="mailto:ba1@sanger.ac.uk" target="_blank">ba1@sanger.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word">Hi Hiram,<div><br></div><div><br></div><div>For the human Y chromosome in Ensembl, we have included DNA sequence (A/G/C/T) for only the unique region. The rest of the chromosome is masked with Ns, which explains how the length of the chromosome matches the GRC chromosome but the composition of the sequence is shifted. The reason we only include the unique region of Y is to make sure that we represent each region of the genome only once. </div>
<div><br></div><div><div>grep \> Homo_sapiens.GRCh37.67.dna.chromosome.Y.fa </div><div>>Y dna:chromosome chromosome:GRCh37:Y:2649521:59034049:1</div></div><div><br></div><div><br></div><div>To add a bit more detail, the Y chromosome has four regions, two of which are unique to Y and two of which are shared with X.</div>
<div>chromosome:GRCh37:Y:1 - 10000 is unique to Y but it's a string of 1000 Ns (Pseudoautosomal region)</div><div>chromosome:GRCh37:Y:10001 - 2649520 is shared with X</div><div>chromosome:GRCh37:Y:2649521- 59034049 is unique to Y</div>
<div>chromosome:GRCh37:Y:59034050 - 59373566 is shared with X</div><div><br></div><div>We store sequence for only the 2 unique regions of Y in our database. The full chromosome Y can be generated on-the-fly by our API, where we stitch in the shared sequence from X. By default our API will fetch only the unique regions of Y however you can request to stitch in the X sequence by setting the 4th argument in the SliceAdaptor to '1' : </div>
<div><span style="color:rgb(128,96,32);font-family:monospace,fixed;font-size:12px;line-height:15px;white-space:pre-wrap">$slice_adaptor->fetch_all('toplevel', undef,0,1)};</span></div><div>The relationship between the shared regions of X and Y are stored in the assembly_exception table.</div>
<div><br></div><div><br></div><div>Hope that helps.</div><div><br></div><div>Cheers,</div><div>Bronwen</div><div><div class="h5"><div><br></div><div><br><div><div>On 8 Jun 2012, at 17:29, Hiram Clawson wrote:</div><br><blockquote type="cite">
<div>Good Morning Ensembl:<br><br>A user reported to UCSC that the GRCh37/hg19 chrY sequence at UCSC is<br>different from the chrY sequence at Ensembl. I picked up the v67<br>chrY sequence from Ensembl and compared it to the UCSC chrY and<br>
the GRCh37 chrY sequence and Ensembl has a different sequence.<br>I checked previous versions of chrY from Ensembl and they remain<br>the same, so it isn't a patched sequence. Anyone know what<br>the story is here ?<br>
<br>--Hiram<br><br>faCount composition measure of chrY sequence from genbank, UCSC and Ensembl:<br><br>#seq len A C G T N cpg<br>CM000686.1 59373566 7667625 5099171 5153288 7733482 33720000 217906<br>
hg19.chrY 59373566 7667625 5099171 5153288 7733482 33720000 217906<br>Y.v67 59373566 6965778 4475138 4518436 7025177 36389037 163434<br><br>_______________________________________________<br>Dev mailing list <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>
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<br></blockquote></div><br><br clear="all"><div><br></div>-- <br>Bert Overduin, Ph.D.<br>Vertebrate Genomics Team<br><br>EMBL - European Bioinformatics Institute<br>Wellcome Trust Genome Campus<br>Hinxton, Cambridge CB10 1SD<br>
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