Hi Jim,

Thanks for the reply. I can get it to work even with the 2 without the quotes. But how do I get the values that I want (E-value, mismatches etc.) from the object returned by blastSequences? 

many thanks!


________________________________
 From: James W. MacDonald <jmacdon@uw.edu>

Cc: bioc <bioconductor@stat.math.ethz.ch> 
Sent: Friday, August 31, 2012 3:09 PM
Subject: Re: [BioC] BLAST - annotate package?

Hi Tim,

Try changing the hitListSize to character:

> blastSequences(x = 
"CAGTTTCTTGAGTCTGATTAATTCAGGTTTCGGGGT",hitListSize="2")
[[1]]
DNAMultipleAlignment with 2 rows and 36 columns
      aln
[1] CAGTTTCTTGAGTCTGATTAATTCAGGTTTCGGGGT
[2] CAGTTTCTTGAGTCTGATTAATTCAGGTTTCGGGGT

[[2]]
DNAMultipleAlignment with 2 rows and 36 columns
      aln
[1] CAGTTTCTTGAGTCTGATTAATTCAGGTTTCGGGGT
[2] CAGTTTCTTGAGTCTGATTAATTCAGGTTTCGGGGT


Best,

Jim



On 8/31/2012 2:44 PM, Tim Smith wrote:
> Hi,
>
[[elided Yahoo spam]]
>
> I am trying to do BLAST (dna-nucleotide) for a sequence. I want to a sequence with the rhesus organism. I would like to get the following values:
>
> 1. Score (bits)
> 2. E-value
> 3. # Matches
>
>
> I am trying to use the 'annotate' package with the following code:
>
> library(annotate)
> xx<- blastSequences(x = "CAGTTTCTTGAGTCTGATTAATTCAGGTTTCGGGGT",hitListSize=2,program = "blastn")
>
>
> Can (how?) I get the values that I want from the object returned? If not, which package/function should I be using? Also, is there a website where I can get the abbreviations for the databases (e.g. is rhesus = 'rh'?)?
>
> Any pointers in the right direction would be highly appreciated
>
>
> many thanks
>     [[alternative HTML version deleted]]
>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
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