[Bioperl-l] Common elements within two set of miRNAs

Juan Jovel jovel_juan at hotmail.com
Thu Jan 5 12:55:16 EST 2012



Not clear to me what you want to do. I guess there are two options: (1) you want to profile mature miRNAs abundance? or (2) you want to profile miRNA transcripts? Allowing up to two mismatches.  In either case, you can align your libraries to the miRNAs hairpins using any aligner (Bowtie, Soap, etc).
However, since 454 libraries are 'relatively' small, you can also do this by stand-alone blast, and after that you parse your results with the searchIO module from BioPerl (two allow a max of 2 mismatches).



> Date: Thu, 5 Jan 2012 02:11:02 -0800
> From: casaburi at ceinge.unina.it
> To: Bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l]  Common elements within two set of miRNAs
> 
> 
> Hi all,  
> 
> i have two set of miRNAs from a 454 run. Now my question is how i can
> clusterize common elements from the two set ? For "common" i mean sequences
> that differ at most by 2 nucleotides ! Is there any tool that can do this
> automatically ?  
> 
> Thank you 
> -- 
> View this message in context: http://old.nabble.com/Common-elements-within-two-set-of-miRNAs-tp33084750p33084750.html
> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
> 
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