[BiO BB] Clustering small DNA sequences into groups

[Yannick Wurm]

Hi Sam,

here's farfetched hack: if you don't find anything else, you may want  
to think along similar lines
     - replace every base by a tab-delimited number
         eg: acttca   becomes     1    2    4    4    2    1
     - use the resulting file as an input for a clustering algorithm  
which clusters things, such as gene expression data

good luck,

yannick

On Aug 10, 2005, at 06:29, Samantha Fox wrote:

> Well, I had thought that there will be some tools to do what I wanted.
> Maybe I will explain a bit more. Say I have these dna sequences
> tataa, tattta, ttaata, taaaaa, tatata, aattaa,ataaa, tctttc,  
> ttcatt, acttca.
>
> Now maybe some sort of grouping or clustering.... in this small
> example last 3 fall in one group ... somehow...
>
> Any clues !
>
> Samantha
>
>
>>
>> On 8/9/05, Martin Gollery <marty.gollery at gmail.com> wrote:
>>
>>> I believe those sequences are too short for Blastclust. The default
>>> word size is 32.
>>>
>>> Marty
>>>
>>> On 8/9/05, Marcos Oliveira de Carvalho <operon at cbiot.ufrgs.br>  
>>> wrote:
>>>
>>>>
>>>>
>>>> Hi Samantha,
>>>>
>>>> BLASTCLUST can group DNA sequences. Maybe you will need to tweak  
>>>> the
>>>> parameters (almost the same for BLAST). You can get it at the  
>>>> NCBI ftp:
>>>> ftp://ftp.ncbi.nih.gov/blast/
>>>>
>>>> cheers
>>>> Marcos
>>>>
>>>>
>>>>
>>>> On Tue, 09 Aug 2005 14:24:41 -0300, Samantha Fox  
>>>> <bioinfosm at gmail.com>
>>>> 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 ?
>>>>>
>>>>> Thanks,
>>>>>
>>>>> Samantha
>>>>>
>>
>>
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