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<div>Steve,</div>
<div><br></div>
<div>This looks great. Thanks so much for adding the SSR
information. </div>
<div><br></div>
<div>From what I can see, the SSR info includes only those that have
been mapped and characterized by our lab as RM markers. It does
not show SSR hits from the set of SSR-containing sequences released
by Monsanto. Is that true?</div>
<div><br></div>
<div>We have a new batch of SSR markers designed from the Monsanto
sequence, and I'm trying to figure out how to deal with the
nomenclature. In some cases, we have more than one primer pair
designed around the same SSR locus, which presents a challenge in
terms of naming convention. </div>
<div><br></div>
<div>In any case, it would be helpful if I could see all the Monsanto
SSR-containing sequences displayed on the contig viewer. Only
about 1,000 of these SSR's have primer pairs designed or tested for
them (unpublished data at this point) but there are more in the
pipeline. Please see
http://www.rice-research.org/cgi-bin/dow<span
></span>nload.cgi/riceSSR_seq.fasta for a FASTA file of the Monsanto
SSR-containing sequences. I wonder if you could discuss with
Doreen and Lincoln to see if you could position as many of these as
possible onto the contig viewer using the Monsanto assigned
ID's. We would then convert the Monsanto ID's into RM
nomenclature as primer pair information is verified. </div>
<div><br></div>
<div>Thanks, Susan</div>
<div><br></div>
<div><br></div>
<blockquote type="cite" cite>SSR's are on the contig
viewer:</blockquote>
<blockquote type="cite"
cite>http://brie2.cshl.org:8082/perl/contigvie<span
></span>w?clone=AP001168<br>
<br>
You can now search by BACend and by the Genbank accession of<br>
a marker tag:</blockquote>
<blockquote type="cite"
cite>http://brie2.cshl.org:8082/perl/unisearch<span
></span><br>
<br>
<br>
A list of clones with maximal combinations of features<br>
or pile-ups is attached.<br>
<br>
--<br>
Steven Schmidt<br>
snp.cshl.org www.gramene.org<br>
Cold Spring Harbor Laboratory<br>
516-367-6977<br>
<br>
</blockquote>
<blockquote type="cite" cite><a
href="http://brie2.cshl.org:8082/perl/contigview?clone=AB023482"
>AB023482</a> Genes=33 BACends=6 MarkerTag=2 ssr=2<br>
<a
href="http://brie2.cshl.org:8082/perl/contigview?clone=AB026295"
>AB026295</a> Genes=35 BACends=13 MarkerTag=5 ssr=2<br>
<a
href="http://brie2.cshl.org:8082/perl/contigview?clone=AC011806"
>AC011806</a> Genes=23 BACends=0 ssr=3<br>
<a
href="http://brie2.cshl.org:8082/perl/contigview?clone=AC016779"
>AC016779</a> Genes=0 BACends=4 ssr=4<br>
<a
href="http://brie2.cshl.org:8082/perl/contigview?clone=AC079022"
>AC079022</a> Genes=30 BACends=4 MarkerTag=8 ssr=1<br>
<a
href="http://brie2.cshl.org:8082/perl/contigview?clone=AC082644"
>AC082644</a> Genes=30 BACends=13 MarkerTag=7<br>
<a
href="http://brie2.cshl.org:8082/perl/contigview?clone=AJ307662"
>AJ307662</a> Genes=56 BACends=0<br>
<a
href="http://brie2.cshl.org:8082/perl/contigview?clone=AL442115"
>AL442115</a> Genes=30 BACends=11 MarkerTag=11<br>
<a
href="http://brie2.cshl.org:8082/perl/contigview?clone=AL513003"
>AL513003</a> Genes=0 BACends=24 MarkerTag=1 ssr=1<br>
<a
href="http://brie2.cshl.org:8082/perl/contigview?clone=AL513004"
>AL513004</a> Genes=0 BACends=52 MarkerTag=4<br>
<a
href="http://brie2.cshl.org:8082/perl/contigview?clone=AP000391"
>AP000391</a> Genes=27 BACends=20 MarkerTag=3 ssr=2</blockquote>
<blockquote type="cite" cite><a
href="http://brie2.cshl.org:8082/perl/contigview?clone=AP000492"
>AP000492</a> Genes=33 BACends=5 MarkerTag=4 ssr=3<br>
<a
href="http://brie2.cshl.org:8082/perl/contigview?clone=AP001129"
>AP001129</a> Genes=38 BACends=9 ssr=1<br>
<a
href="http://brie2.cshl.org:8082/perl/contigview?clone=AP001168"
>AP001168</a> Genes=28 BACends=18 MarkerTag=4 ssr=3<br>
<a
href="http://brie2.cshl.org:8082/perl/contigview?clone=AP001551"
>AP001551</a> Genes=32 BACends=18 MarkerTag=4<br>
<a
href="http://brie2.cshl.org:8082/perl/contigview?clone=AP002482"
>AP002482</a> Genes=36 BACends=7 MarkerTag=4<br>
<a
href="http://brie2.cshl.org:8082/perl/contigview?clone=AP002540"
>AP002540</a> Genes=34 BACends=6 MarkerTag=8<br>
<a
href="http://brie2.cshl.org:8082/perl/contigview?clone=AP002542"
>AP002542</a> Genes=33 BACends=4 MarkerTag=7 ssr=1<br>
<a
href="http://brie2.cshl.org:8082/perl/contigview?clone=AP002744"
>AP002744</a> Genes=36 BACends=5 MarkerTag=7<br>
<a
href="http://brie2.cshl.org:8082/perl/contigview?clone=AP002819"
>AP002819</a> Genes=26 BACends=21 MarkerTag=4 ssr=1<br>
<a
href="http://brie2.cshl.org:8082/perl/contigview?clone=AP002882"
>AP002882</a> Genes=32 BACends=10 MarkerTag=6<br>
<a
href="http://brie2.cshl.org:8082/perl/contigview?clone=AP002953"
>AP002953</a> Genes=23 BACends=10 MarkerTag=6 ssr=2<br>
<a
href="http://brie2.cshl.org:8082/perl/contigview?clone=AP003047"
>AP003047</a> Genes=23 BACends=43 MarkerTag=1</blockquote>
<blockquote type="cite" cite><a
href="http://brie2.cshl.org:8082/perl/contigview?clone=AP003048"
>AP003048</a> Genes=21 BACends=7 MarkerTag=5<br>
<a
href="http://brie2.cshl.org:8082/perl/contigview?clone=AP003076"
>AP003076</a> Genes=40 BACends=12 MarkerTag=3<br>
<a
href="http://brie2.cshl.org:8082/perl/contigview?clone=AP003277"
>AP003277</a> Genes=33 BACends=29 MarkerTag=2<br>
<a
href="http://brie2.cshl.org:8082/perl/contigview?clone=AP003747"
>AP003747</a> Genes=0 BACends=18 MarkerTag=4<br>
<a
href="http://brie2.cshl.org:8082/perl/contigview?clone=AP003904"
>AP003904</a> Genes=0 BACends=8 MarkerTag=7 ssr=1<br>
<a
href="http://brie2.cshl.org:8082/perl/contigview?clone=AP003989"
>AP003989</a> Genes=0 BACends=0 ssr=4<br>
<a
href="http://brie2.cshl.org:8082/perl/contigview?clone=AP004001"
>AP004001</a> Genes=0 BACends=10 ssr=2<br>
<a
href="http://brie2.cshl.org:8082/perl/contigview?clone=AP004048"
>AP004048</a> Genes=0 BACends=12 MarkerTag=6 ssr=1</blockquote>
<blockquote type="cite" cite><a
href="http://brie2.cshl.org:8082/perl/contigview?clone=AP004065"
>AP004065</a> Genes=0 BACends=5 MarkerTag=3 ssr=3</blockquote>
<div><br></div>
<div>*****************************************<span
></span>*<br>
Susan McCouch<br>
Dept of Plant Breeding<br>
418 Bradfield Hall<br>
Cornell University<br>
Ithaca, NY 14853-1901<br>
Phone: 607-255-0420<br>
Fax: 607-255-6683<br>
E-Mail: srm4@cornell.edu<br>
<br>
*****************************************<span
></span>*</div>
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