I have a set of RM series SSR markers of rice (nearly 100 in number) and I wish to check:
1. Their position in the genome at a single go (preferably with graphical output)
2. If any of these markers a located within genic region or close to genic region (most important)
It will be a great help if any body can suggest any software for these.
Besides, I also want to download the exact physical locus of all the rice genes (having MSU ID). How can I do that?
There are probably much prettier methods, particularly considering the vast resources that have been poured into the analysis of the rice genome. However, I will give you a quick and dirty way to accomplish your goal-
(Using a Linux server or PC with BLAST and Perl installed) You could create a BLAST database (very simple --> formatdb) from the rice reference genome assembly (pseudomolecules or contigs, whatever sequences you wish to locate your markers within. Then, create a FASTA file with your primers (or, even better, the sequences of the amplified fragments...). You can then BLASTN the primer sequences as queries against the reference genome database. If you're using primer sequences, then you'll need to lower the cut-off value, and I recommend taking the top 3 hits or so.
Once you have the BLASTN output, a simple Perl script can extract the start locations for each sequence. You can then compare the hits for each marker's forward and reverse primer - obviously, they should be approximately as far apart as the expected fragment size and on opposite strands.
For the genes, I assume that the rice genome website has a list of annotated genes and their genomic positions readily available for download. I recommend that you spend some time getting to know the site and the available resources there (see the link I left here).
http://rice.plantbiology.msu.edu/downloads_gad.shtml
ftp://ftp.plantbiology.msu.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/
Plant enseble genome browser will provide you every details. Here is the link http://plants.ensembl.org/index.html
You can search it on GRAMENE. All information about rice markers, their position in the chromosome and whether it is linked with any gene or not is available there.
use the gbrowse in rap-db database, switch on gene and marker tracks to view them together. If you want markers on a particular gene, use the protein sequence and do a tblastn to locate the protein to the genome and from there you can viw the markers around the gene
CLC Workbench can find them all but first you need to download and import a reference genome .... just google it.
I normally use this site: http://qtaro.abr.affrc.go.jp
Hope you find it useful.
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