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Hi,<br>
<br>
Within Ensembl, the LRG sequences can be found by searching for e.g.
the LRG identifier or the HGNC name of a gene for which an LRG
record exists. Since the LRG sequences are not part of the genome
assembly, they have their own dedicated display, e.g. <a
class="moz-txt-link-freetext"
href="http://www.ensembl.org/Homo_sapiens/LRG/Summary?lrg=LRG_1">http://www.ensembl.org/Homo_sapiens/LRG/Summary?lrg=LRG_1</a>.
The LRG display is till very much under development and currently
does not have the same functionality as the genome assembly display
but we are constantly working on improving the functionality. You
can e.g. view the LRG sequence annotated with the transcripts that
are defined on the LRG along with projections of SNPs. The
transcript annotations and sequences are also obtainable through the
Perl API.<br>
<br>
At the moment, you can not view the gene annotations from the genome
assembly in the context of LRGs but for the upcoming Ensembl release
60, we aim to project and display this information. Note that at the
moment, this projection is also available within the LRG XML files
that are available for download and display on the LRG website, e.g.
<a class="moz-txt-link-freetext"
href="http://www.lrg-sequence.org/LRG/LRG_1">http://www.lrg-sequence.org/LRG/LRG_1</a>.<br>
<br>
Any further suggestions on useful functionality on the LRG display
within Ensembl are most welcome!<br>
<br>
Also, note that if you search for an LRG on the LRG website and
follow the link to the Ensembl browser, there will be a GFF file
attached to the display that indicates the structure of the LRG
transcript(s) on the genome assembly (e.g. <a
class="moz-txt-link-freetext"
href="http://www.ensembl.org/Homo_sapiens/Location/View?r=17:48259457-48284000&contigviewbottom=url:ftp://ftp.ebi.ac.uk/pub/databases/lrgex/.ensembl_internal/LRG_1.xml.gff=labels">http://www.ensembl.org/Homo_sapiens/Location/View?r=17:48259457-48284000&contigviewbottom=url:ftp://ftp.ebi.ac.uk/pub/databases/lrgex/.ensembl_internal/LRG_1.xml.gff=labels</a>).<br>
<br>
Thanks<br>
/Pontus Larsson - Ensembl Variation<br>
<br>
<br>
On 13/10/2010 18:53, Bio X2Y wrote:
<blockquote
cite="mid:AANLkTimft6MQNNPoO64QtrFAiz9vZ0AhVUSMCiofB33j@mail.gmail.com"
type="cite">Hi,
<div><br>
</div>
<div>The LRG sequences gene annotations seem to be dropped from
Ensembl 59. Is this intentional?</div>
<div><br>
</div>
<div>Thanks.</div>
<div><br>
</div>
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