These commands are straight from the Biostrings; PatternMatch manual.
Could not find any help online.
Any advice on the key 86 error??


Otherwise has anyone do genomic BLAST from within R. Any advice on the
best path.... Use Blastcl3 ? ,another standalone blast , ?
Maybe a 1000 or do short sequences to blast....

Thanks in advance 
Paul

CODE

>  cI <- Mmusculus$chr13
> length(cI)
[1] 120614378
> class(cI)
[1] "DNAString"
attr(,"package")
[1] "Biostrings"



>  p <- "UUACAGUUGUUCAACCAGUUACU"

*********** ERROR****************
>  matchPattern(p, cI, mismatch = 0)
Error in CharBuffer.write(data, 1, length, value = src, enc = lkup) : 
        key 85 not in lookup table

*************************************

> sessionInfo()
R version 2.5.0 (2007-04-23) 
i386-pc-mingw32 

locale:
LC_COLLATE=English_Australia.1252;LC_CTYPE=English_Australia.1252;LC_MON
ETARY=English_Australia.1252;LC_NUMERIC=C;LC_TIME=English_Australia.1252

attached base packages:
[1] "tools"     "stats"     "graphics"  "grDevices" "utils"
"datasets" 
[7] "methods"   "base"     

other attached packages:
BSgenome.Mmusculus.UCSC.mm8                    BSgenome 
                    "1.2.0"                     "1.4.0" 
                    Biobase                  Biostrings 
                   "1.14.0"                     "2.4.5" 


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