[BioPython] How to use Bio.cluster Module to assembly dna sequences

[Jose Blanca]

Hi,
I don't know the details of your sequences, but for the assembly that you want 
to do there could be better methods. I have done this kind of assemblies with 
ESTs sequences and for that porpouse I have used cap3 or tgicl.
Best regards,

Jose Blanca

On Thursday 27 March 2008 18:33:55 Bruno Santos wrote:
> Hi,
>
> This question is a little bit more generic so I really don't know if anyone
> in the mailing may help me.
>
> I have a fasta file with thousands of reads obtained by a sequencing run,
> in this fasta file I know I have several copies of the same sequences but
> their size and some nucleotides inside it can change. So I need to group
> them together using clustering so then I can create a consensus sequence
> for each group.
>
> I am trying to achieve this by align all the sequences using clustalw-mpi
> and the I run dnadist from phylip to obtain a matrix of distances between
> the sequences. Now I need to use clustering to group the sequences based on
> these values and for that I am trying to use Bio.cluster to achieve this.
> Can anyone help me to choose the clustering method I should use and how can
> I submit this kind of data to that method?
>
>
>
> Sincerely,
>
> Bruno Santos
>
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-- 
Jose M. Blanca Postigo
Instituto Universitario de Conservacion y
Mejora de la Agrodiversidad Valenciana (COMAV)
Universidad Politecnica de Valencia (UPV)
Edificio CPI (Ciudad Politecnica de la Innovacion), 8E
46022 Valencia (SPAIN)
Tlf.:+34-96-3877000 (ext 88473)