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<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman"
size=3>I have some questions about using Marker<SPAN
class=290362216-20092011>_Feature</SPAN> annotations <SPAN
style="mso-spacerun: yes"> </SPAN>in Ensembl. We are thinking about cross
referencing Marker<SPAN class=290362216-20092011>s</SPAN> from some of our data
resources<SPAN class=290362216-20092011>, giving us a link in from genetic maps
to the Ensembl annotated genome. I can't find much detailed documentation about
the creation and use of Marker_Features so would appreciate if anyone can give
me some specific information.</SPAN></FONT></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><o:p><FONT face="Times New Roman"
size=3></FONT></o:p> </P>
<OL style="MARGIN-TOP: 0cm" type=1>
<LI class=MsoNormal
style="MARGIN: 0cm 0cm 0pt; mso-list: l0 level1 lfo1; tab-stops: list 36.0pt"><FONT
face="Times New Roman"><FONT size=3>I take it that for each genome build (or
ensembl release?) the ePCR analysis<SPAN class=290362216-20092011> of Marker
primer pairs</SPAN> is done afresh – rather than mapping the previous
marker coordinates to a new build?<SPAN class=290362216-20092011> and that
there is a cutoff threshold to discard multiple mappings (map
weight > 3?).<BR></SPAN></FONT></FONT>
<LI class=MsoNormal
style="MARGIN: 0cm 0cm 0pt; mso-list: l0 level1 lfo1; tab-stops: list 36.0pt"><FONT
face="Times New Roman" size=3>I had assumed that the Marker ePCR would be
<SPAN style="mso-spacerun: yes"> </SPAN>performed on the assembled
chromosome/toplevel assembly: but there is no entry ‘marker.build = toplevel’
in table ‘meta’ analagous to ‘gene.build=toplevel’. Furthermore, it looks like
(in the case of cows and humans where I have looked) a very small proportion
of the markers are mapped on to the next level down (scaffold, supercontig or
contig). Obviou<SPAN class=290362216-20092011>sly</SPAN> these don’t show up
on the chromosomes – but can be found by searching <SPAN
class=290362216-20092011>by marker name </SPAN>and are displayed on the
contig.</FONT><o:p><FONT face="Times New Roman" size=3> <BR></FONT></o:p>
<LI class=MsoNormal
style="MARGIN: 0cm 0cm 0pt; mso-list: l0 level1 lfo1; tab-stops: list 36.0pt"><FONT
face="Times New Roman" size=3>When I delve into the PerlAPI sourcecode it
looks to me like marker features are always searched on the toplevel
coordinate system, but also on other CS levels. Presumably this unpleasantness
is because there is no use of a ‘build’ entry in table ‘meta’, and to catch
any markers mapped to the supercontigs etc.<BR></FONT>
<LI class=MsoNormal
style="MARGIN: 0cm 0cm 0pt; mso-list: l0 level1 lfo1; tab-stops: list 36.0pt"><FONT
face="Times New Roman" size=3>Which different resources of Markers are
imported into Ensembl? Is this decided per species? Is UniSTS always imported
for every species?<BR></FONT>
<LI class=MsoNormal
style="MARGIN: 0cm 0cm 0pt; mso-list: l0 level1 lfo1; tab-stops: list 36.0pt"><FONT
face="Times New Roman" size=3>If we want add markers to the Ensembl pipeline,
is the correct approach to add markers and maps to UniSTS database, and will
these then be pulled automatically into future Ensembl release builds?
</FONT></LI></OL></FONT></DIV>
<DIV><SPAN class=290362216-20092011><FONT face=Arial size=2>Thanks for any
help...or pointers to more documentation.</FONT></SPAN></DIV>
<DIV align=left>
<P align=left><STRONG><B><FONT face=Arial color=navy><SPAN
style="FONT-SIZE: 12pt; COLOR: navy; FONT-FAMILY: Arial">Trevor Paterson
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