Contig viewer (on chevre)

Tue Oct 16 08:45:05 EDT 2001

Steve,

This looks great.  Thanks so much for adding the SSR information.

 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?

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.

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(unpublished data at this point) but there are more in the pipeline.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/download.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.

Thanks, Susan

>SSR's are on the contig viewer:
>http://brie2.cshl.org:8082/perl/contigview?clone=AP001168
>
>You can now search by BACend and by the Genbank accession of
>a marker tag:
>http://brie2.cshl.org:8082/perl/unisearch
>
>
>A list of clones with maximal combinations of features
>or pile-ups is attached.
>
>--
>Steven Schmidt
>snp.cshl.org     www.gramene.org
>Cold Spring Harbor Laboratory
>516-367-6977
>
>
><http://brie2.cshl.org:8082/perl/contigview?clone=AB023482>AB023482 
>Genes=33 BACends=6 MarkerTag=2 ssr=2
><http://brie2.cshl.org:8082/perl/contigview?clone=AB026295>AB026295 
>Genes=35 BACends=13 MarkerTag=5 ssr=2
><http://brie2.cshl.org:8082/perl/contigview?clone=AC011806>AC011806 
>Genes=23 BACends=0 ssr=3
><http://brie2.cshl.org:8082/perl/contigview?clone=AC016779>AC016779 
>Genes=0 BACends=4 ssr=4
><http://brie2.cshl.org:8082/perl/contigview?clone=AC079022>AC079022 
>Genes=30 BACends=4 MarkerTag=8 ssr=1
><http://brie2.cshl.org:8082/perl/contigview?clone=AC082644>AC082644 
>Genes=30 BACends=13 MarkerTag=7
><http://brie2.cshl.org:8082/perl/contigview?clone=AJ307662>AJ307662 
>Genes=56 BACends=0
><http://brie2.cshl.org:8082/perl/contigview?clone=AL442115>AL442115 
>Genes=30 BACends=11 MarkerTag=11
><http://brie2.cshl.org:8082/perl/contigview?clone=AL513003>AL513003 
>Genes=0 BACends=24 MarkerTag=1 ssr=1
><http://brie2.cshl.org:8082/perl/contigview?clone=AL513004>AL513004 
>Genes=0 BACends=52 MarkerTag=4
><http://brie2.cshl.org:8082/perl/contigview?clone=AP000391>AP000391 
>Genes=27 BACends=20 MarkerTag=3 ssr=2
><http://brie2.cshl.org:8082/perl/contigview?clone=AP000492>AP000492 
>Genes=33 BACends=5 MarkerTag=4 ssr=3
><http://brie2.cshl.org:8082/perl/contigview?clone=AP001129>AP001129 
>Genes=38 BACends=9 ssr=1
><http://brie2.cshl.org:8082/perl/contigview?clone=AP001168>AP001168 
>Genes=28 BACends=18 MarkerTag=4 ssr=3
><http://brie2.cshl.org:8082/perl/contigview?clone=AP001551>AP001551 
>Genes=32 BACends=18 MarkerTag=4
><http://brie2.cshl.org:8082/perl/contigview?clone=AP002482>AP002482 
>Genes=36 BACends=7 MarkerTag=4
><http://brie2.cshl.org:8082/perl/contigview?clone=AP002540>AP002540 
>Genes=34 BACends=6 MarkerTag=8
><http://brie2.cshl.org:8082/perl/contigview?clone=AP002542>AP002542 
>Genes=33 BACends=4 MarkerTag=7 ssr=1
><http://brie2.cshl.org:8082/perl/contigview?clone=AP002744>AP002744 
>Genes=36 BACends=5 MarkerTag=7
><http://brie2.cshl.org:8082/perl/contigview?clone=AP002819>AP002819 
>Genes=26 BACends=21 MarkerTag=4 ssr=1
><http://brie2.cshl.org:8082/perl/contigview?clone=AP002882>AP002882 
>Genes=32 BACends=10 MarkerTag=6
><http://brie2.cshl.org:8082/perl/contigview?clone=AP002953>AP002953 
>Genes=23 BACends=10 MarkerTag=6 ssr=2
><http://brie2.cshl.org:8082/perl/contigview?clone=AP003047>AP003047 
>Genes=23 BACends=43 MarkerTag=1
><http://brie2.cshl.org:8082/perl/contigview?clone=AP003048>AP003048 
>Genes=21 BACends=7 MarkerTag=5
><http://brie2.cshl.org:8082/perl/contigview?clone=AP003076>AP003076 
>Genes=40 BACends=12 MarkerTag=3
><http://brie2.cshl.org:8082/perl/contigview?clone=AP003277>AP003277 
>Genes=33 BACends=29 MarkerTag=2
><http://brie2.cshl.org:8082/perl/contigview?clone=AP003747>AP003747 
>Genes=0 BACends=18 MarkerTag=4
><http://brie2.cshl.org:8082/perl/contigview?clone=AP003904>AP003904 
>Genes=0 BACends=8 MarkerTag=7 ssr=1
><http://brie2.cshl.org:8082/perl/contigview?clone=AP003989>AP003989 
>Genes=0 BACends=0 ssr=4
><http://brie2.cshl.org:8082/perl/contigview?clone=AP004001>AP004001 
>Genes=0 BACends=10 ssr=2
><http://brie2.cshl.org:8082/perl/contigview?clone=AP004048>AP004048 
>Genes=0 BACends=12 MarkerTag=6 ssr=1
><http://brie2.cshl.org:8082/perl/contigview?clone=AP004065>AP004065 
>Genes=0 BACends=5 MarkerTag=3 ssr=3

******************************************
Susan McCouch
Dept of Plant Breeding
418 Bradfield Hall
Cornell University
Ithaca, NY  14853-1901
Phone: 607-255-0420
Fax: 607-255-6683
E-Mail: srm4 at cornell.edu

******************************************
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