[Arabidopsis] RE: polymorphism between Ws-2 and Col on chr1

Nicholas Provart via arab-gen%40net.bio.net (by nicholas.provart At utoronto.ca)
Wed Dec 6 14:01:56 EST 2006


Hi Xuewen,

Using Magnus Nordborg's high quality sequence data from ~500 genomic regions
across 96 Arabidopsis accessions we have computed all possible CAPS markers
relative to the Col-0 background and deposited these in our MarkerTracker
database, available here:

http://bbc.botany.utoronto.ca/markertracker/ 

It seems there isn't anything in that region for the Ws-2 sequences
available (not that many) but there are several for Ler x Col-0, some of
which might work. 

Alternately, there are lots of Ws (at least Ws-0) ESTs available and you can
Blast2Seq ones from the required region against the ones from Col-0 and then
use our BlastDigester tool at 

http://bbc.botany.utoronto.ca/ntools/cgi-bin/ntools_blast_digester.cgi

to identify potential snip-SNPs to generate CAPS markers.

Nick
.........................................
Nicholas Provart, PhD
Assistant Professor, Plant Bioinformatics
Director, Program in Genome Biology and Bioinformatics
Member, Centre for the Analysis of Genome Evolution and Function
Rm 3051, Dept. of Cell and Systems Biology, Uni. Toronto
25 Willcocks St., Toronto, ON. M5S 3B2. CANADA

Tel. (+1) (416) 978-7141, Fax. (+1) (416) 978-5878
URL. http://www.csb.utoronto.ca/faculty/provart/
Arabidopsis Tools. http://bbc.botany.utoronto.ca   
email. nicholas.provart At utoronto.ca
TTC. Spadina LRT, Willcocks St.

>
>Hi, everyone
>
>
>
>Does anyone know any polymorphism between Ws-2 and Col in the region of
>(Nt sequence position) 3041125bp to 3224463bp on chr1? I am doing a
>mapping for the photo-morphogenesis mutant in Arabidopsis?
>
>
>
>Thanks.
>
>
>
>Xuewen Wang
>
>School of biology
>
>Royal Holloway Uni of London
>
>UK TW20 OEx
>
>Email: x.w.wang At rhul.ac.uk
>
>
>
>------------------------------
>
>_______________________________________________
>Arab-gen mailing list
>Arab-gen At net.bio.net
>http://www.bio.net/biomail/listinfo/arab-gen
>
>End of Arab-gen Digest, Vol 20, Issue 4
>***************************************




More information about the Arab-gen mailing list