[BiO BB] Clustering small DNA sequences into groups

[Iddo Friedberg]

CD-HIT does not work on DNA, or short sequences for that matter..


Dan Bolser wrote:

>On Tue, 9 Aug 2005, Samantha Fox wrote:
>
>  
>
>>Hi,
>>
>>I have a set of small DNA sequences (about 40) 6-10 bp, and wish to
>>group them into clusters based on sequence.
>>
>>Any suggestions for doing that ?
>>    
>>
>
>I never tried using CD-HIT to cluster DNA, but it should work (you will
>have to alter the 'throwaway' length to something like 4 to stop all your
>sequences being filterd as too short. 
>
>I found blastclust (which can be explicitly set to cluster
>DNA) automatically ignores any protein sequence of less than 30
>residues. While it could cluster those together (100% identical for
>example) it always seems to put any protein fragment less than 30 residues
>into a new cluster.
>
>Not sure if the behaviour is the same in DNA mode.
>
>
>  
>
>>Thanks,
>>
>>Samantha
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>>    
>>
>
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-- 

Iddo Friedberg, Ph.D.
The Burnham Institute
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