[BioC] BioStrings questions

[rcaloger]

Hi,
In my onechannelGUI package I am developing a section related to 
Affymetrix exon array analysis, creating few functions that allow the 
association of exon-level Probe Selection Region (PSR) to refseq

1st question:
I have implemented a function that blast a list of PSR sequences over 
all refseq.
However, I would like to know if there is any way of doing something 
similar using the Biostring package.
I tried the pairwiseAlignment function but it is quite slow compared to 
blast.

2nd question:
 there is any way of merging two DNAStringSets ?

Cheers
Raffaele



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Prof. Raffaele A. Calogero
Bioinformatics and Genomics Unit
Dipartimento di Scienze Cliniche e Biologiche
c/o Az. Ospedaliera S. Luigi
Regione Gonzole 10, Orbassano
10043 Torino
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Mobile ++39 3333827080
email: raffaele.calogero at unito.it
       raffaele[dot]calogero[at]gmail[dot]com
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