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

Florent Angly florent.angly at gmail.com
Thu Jan 5 18:08:52 EST 2012


Clustering software such as CD-HIT or UCLUST comes to mind.
Florent

On 06/01/12 04:19, Chris Fields wrote:
> 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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