oryzasnp.plantbiology.msu.edu oryzasnp.plantbiology.msu.edu

oryzasnp.plantbiology.msu.edu

OryzaSNP @ MSU

OryzaSNP @ MSU is a resource for rice SNPs for use by the rice research community.

http://oryzasnp.plantbiology.msu.edu/

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OryzaSNP @ MSU | oryzasnp.plantbiology.msu.edu Reviews
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OryzaSNP @ MSU is a resource for rice SNPs for use by the rice research community.
<META>
KEYWORDS
1 rice
2 SNP
3 SNPs
4 polymorphism
5 resequencing
6 Perlegen
7 cultivars
8 TIGR
9 MSU
10 IRGSP
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oryzasnp @msu,search tools,browsers,people,links,download,oryzasnp project,snp identification project,or irgsp based
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OryzaSNP @ MSU | oryzasnp.plantbiology.msu.edu Reviews

https://oryzasnp.plantbiology.msu.edu

OryzaSNP @ MSU is a resource for rice SNPs for use by the rice research community.

INTERNAL PAGES

oryzasnp.plantbiology.msu.edu oryzasnp.plantbiology.msu.edu
1

OryzaSNP People

http://oryzasnp.plantbiology.msu.edu/people.html

Researchers Associated with OryzaSNP. International Rice Research Institute, Genetics. Colorado State University, Bioagr. Sciences and Pest Management. Max Planck Institute, Friedrich Miescher Laboratory of the Max Planck Society. Max Planck Institute, Department of Molecular Biology. Cornell University, Dept. of Biological Stat. and Comp. Biol. McGill University, Department of Biology. Perlegen Sciences, Genetics. Michigan State University, Plant Biology Department. Photo courtesy Ariel Javellana/IRRI.

2

Links

http://oryzasnp.plantbiology.msu.edu/links.html

Links Associated with OryzaSNP. OryzaSNP Project at IRRI. OryzaSNP Genome Browser at IRRI. MSU Rice Genome Annotation Project (formerly at TIGR). Rice Annotation Project (RAP) Database. Rice research at the Buell lab at MSU. MSU Biofuel Feedstock Genomics Resource. Weigel Group at Max Planck Institute. International Rice Research Institute. Original template by Darjan Panic and Brian Green. Photo courtesy Ariel Javellana/IRRI.

3

Search Pages

http://oryzasnp.plantbiology.msu.edu/tools.html

Links to OryzaSNP Search Pages. Search for Perlegen Identified SNPs Between Two Coordinates on One Chromosome. Search Multiple Cultivars for SNPs. Find Polymorphic Positions Between Two Cultivars. Find the Classifications for a List of SNPs. Find the SNP Positions Within a List of Genes. Find the Base Calls for Cultivars at SNP Positions. Obtain the Sequences Surrounding a Set of SNPs. Original template by Darjan Panic and Brian Green. Photo courtesy Ariel Javellana/IRRI.

4

Rice SNP Browser - IRGSP Pseudomolecules

http://oryzasnp.plantbiology.msu.edu/cgi-bin/gbrowse/osa_snp_irgsp

Recenter on this region. Dump selection as FASTA. OryzaSNP Genome Browser - IRGSP Pseudomolecules. Search using a sequence name, gene name, locus, or other landmark. The wildcard character * is allowed. Click one of the rulers to center on a location, or click and drag to select a region. Use the Scroll/Zoom buttons to change magnification and position. Upload your own data]. Download Decorated FASTA File. Rice SNP Browser - IRGSP Pseudomolecules. Rice SNP Browser - MSU/TIGR Pseudomolecules. Swarna Perle...

5

OryzaSNP Genome Browsers

http://oryzasnp.plantbiology.msu.edu/browsers.html

SNPs were identified using an array-based resequencing that used the IRGSP Oryza sativa. Cv Nipponbare genomic sequence as a reference. All SNPs that have been identified by the OryzaSNP project have been mapped to both the IRGSP rice pseudomolecules and to the TIGR/MSU rice pseudomolecules. Annotations of the SNPs have been made relative to the RAP rice gene models. And relative to the TIGR/MSU rice gene models. Two genome browsers are available for viewing the OryzaSNP data.

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