Dear Mailing List,
 
Why does pairwiseAlignment() generate different outcomes for the same input 
 sequences defined differently in terms of classes (see showMethods below):
 
for 
 
pattern="character", subject="character"

vs.
 
pattern="DNAString", subject="DNAString"
 
?
 
It generates the same outcomes for the case of 
 
 
pattern="character", subject="character"
 
vs.
 
pattern="character", subject="DNAString"


It looks like a bug. 
 
Thanks
 
Alex
 
 
 
 
 
 
#showMethods("pairwiseAlignment")
#Function: pairwiseAlignment (package Biostrings)
#pattern="character",  subject="character"
#pattern="character",  subject="DNAString"
#    (inherited from: pattern="character",  subject="XString")
#pattern="DNAString", subject="DNAString"

> pattern.1
50-letter "DNAString" instance
seq:  CTGCCATGGCAAAGCTCGCTGCCTCAGAGGCCGCCACAATGGTTGCGCAC
> pattern.2
[1]  "CTGCCATGGCAAAGCTCGCTGCCTCAGAGGCCGCCACAATGGTTGCGCAC"
> subject.1
543-letter "DNAString" instance
seq:  
AAAAAAAAAAAAAAAAAAAAATGAAATCCGAACTTCTTGGAGCCTCGTCTGAAGGCCATCTCGGCTCTTCAGATT...CAGTCAACAAGTTCCAACGGGACTAGATTACGGGGCGTATACGCCGTACGGCCAGGCCAGTAGTTACG
CGTCGT
>  subject.2
[1]  
"AAAAAAAAAAAAAAAAAAAAATGAAATCCGAACTTCTTGGAGCCTCGTCTGAAGGCCATCTCGGCTCTTCAGATTCGCCCTTCGTCAGCGACGCTCTGGCTGCCGTCACCGGTGACTACCAATCGGCCTACGCTGCTTCCTATTAC
AGCAGCGCGATGCAGGCCTACAATAGTCAATCGACGTCGGCCTACATGCCAAGCAGTGGATTCTATAATGGCGCAT
CTTCGCAGACGCCCTACGGAGTCCTGGCGCCCTCCACTTACACAACGATGGGCGTTCCCAGTACAAGAGGTTTAGG
CCAACAATGTAAAAATGGACAATCATTAGCACAAACGCCTCCGTATTTGAGCTCGTACGGGTCGGCATTCGGTGGT
GTCACAGCCAGCAGTTCGCCTTCGGGTCCACCCGCCTACGCGTCCGCTTATGGATCGGCATACAATAGCGCCACCG
CCGCCCAATCGTTCACCAACAGTCAACAAGTTCCAACGGGACTAGATTACGGGGCGTATACGCCGTACGGCCAGGC
CAGTAGTTACGCGTCGT"
>  

>  
pairwiseAlignment(pattern=pattern.1,subject=subject.1,type="global-local")
Global-Local  PairwiseAlignedFixedSubject (1 of 1)
pattern:   [1]  CTGCCATGGCAAAGCTCGCTGCCTCAGAGGCCGCCACAATGGTTGCGCAC 
subject: [429]  TCGGCATACAATAGC--GCCACC------GCCGCC-CAATCGTT---CAC 
score: -91.50367 
>  
pairwiseAlignment(pattern=pattern.2,subject=subject.2,type="global-local")
Global-Local  PairwiseAlignedFixedSubject (1 of 1)
pattern:  [1]  CTGC--CATGGCAAAGCTC--GCTGCC-TCAGAGGCCGCCAC-AATGGTTGCGCAC 
subject: [80]  CTTCGTCA--GCGACGCTCTGGCTGCCGTCACCGGTGACTACCAATCG--GCCTAC 
score: 95.69296  
>  
pairwiseAlignment(pattern=pattern.2,subject=subject.1,type="global-local")
Global-Local  PairwiseAlignedFixedSubject (1 of 1)
pattern:   [1]  CTGCCATGGCAAAGCTCGCTGCCTCAGAGGCCGCCACAATGGTTGCGCAC 
subject: [429]  TCGGCATACAATAGC--GCCACC------GCCGCC-CAATCGTT---CAC 
score: -91.50367 
 
> sessionInfo()
R version 2.12.2 (2011-02-25)
Platform:  i386-pc-mingw32/i386 (32-bit)
 
locale:
[1] LC_COLLATE=English_United States.1252   LC_CTYPE=English_United 
States.1252    LC_MONETARY=English_United  States.1252
[4]  LC_NUMERIC=C                            LC_TIME=English_United 
States.1252    
 
attached base packages:
[1] stats     graphics   grDevices utils     datasets  methods    base     
 
other attached packages:
[1] altcdfenvs_2.12.0 hypergraph_1.22.0  graph_1.28.0      
makecdfenv_1.28.0  affy_1.28.0       Biobase_2.10.0     GeneR_2.20.0      seqinr_3.0-1      
[9] Biostrings_2.18.4 IRanges_1.8.9      limma_3.6.9      
 
loaded via a namespace (and not attached):
[1]  affyio_1.18.0          preprocessCore_1.12.0  tools_2.12.2         




###############################
 
Nutritional Sciences and Toxicology,
119 Morgan Hall
UC.Berkeley,CA 94720
 

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