small RNA target sequence - (May/09/2008 )

HI
a gene has its pseudogene version created by just a deletion of some base pairs. If i want to find whether this is done by a small RNA by RNA interferrence what should i do how to find a small RNA target site in my mRNA? just doing a blast with small RNA database...or any other method...can you provide some tool link?? the genome is of rice....Your reply will be a great help
thankss

Why do you think a pseudogene can be created by small rna targeting? Would you suggest a reference about that?

Although there are probably better ways, you can do your search as follow:

-download all miRNAs from the miRbase (http://microrna.sanger.ac.uk/sequences/ftp.shtml), it's a pretty small fasta file
-dowload the miRanda software from here (http://www.microrna.org/microrna/getDownloads.do), it's easy to use in windows, just need a java interface
-load the fasta file of the mirnas and a fasta file of your gene (using the command upload UTRs)
-run miRanda setting scaling factor 1, gap open penalty -20, gap extend penalty -80, use simplified model, quite mode, disable thermodynamics
-save the output in a notepad. You can easily score the results with the search windows command, looking, for instance, for the word 'score'.

these settings usually allow only one bulged nt in the pairing. if you want to relax the stringency, increase gap open penalty. You can also modify the score threshold if you get too much or too few matches. Try first with some known rice mRNA target, just to see if it works, but it should ...

good luck,
bye