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

Chris Fields cjfields at illinois.edu
Thu Jan 5 13:19:35 EST 2012


You can use mcl for this, see:

http://micans.org/mcl/man/clmprotocols.html#blast

If you only want a difference of 2 nucleotides, it's probably worth 
pre-parsing the data to filter the information you need (as Juan 
suggests, Bio::SearchIO can do this), getting retained hits it into a 
form that mcl can use.

chris

On 01/05/2012 11:55 AM, Juan Jovel wrote:
>
> 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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