[R] sequence clustering and assembly

[Martin Morgan]

Hi Bogdan --

On 04/14/2010 08:19 PM, Bogdan Tanasa wrote:
> Dear all,
> 
> please could you suggest any R functions or packages (or external
> programs), that
likely you'll have more luck on the Bioconductor mailing list,

http://bioconductor.org/docs/mailList.html

but...

> a. take as input a large number (> 10 000) of short 20-30 nt
> sequences, and do sequence assembly, to reconstruct larger (extended)
> 30-50 sequences ?

I don't know of any sequence assemblers in R; velvet would be a first
stop third party tool but it sounds like you have some fairly specific
requirements....

> b. take as input a larger number of sequences (100 000 - 1 mil) and
> cluster these sequences in distinct classes based on the sequence
> similarity  ?

The Biostrings package has various functions to calculate edit distance,
which might form the input to familiar R clustering algorithms. See
installation instructions at

http://www.bioconductor.org/packages/release/bioc/html/Biostrings.html

This thread

https://stat.ethz.ch/pipermail/bioconductor/2010-March/032580.html

might suggest some directions.

Martin

> 
> thanks a lot,
> 
> bogdan
> 
> [[alternative HTML version deleted]]
> 
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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