Hi Martin,
 
Thanks for the clarification. Does the variant of   pattern="DNAString", 
subject="DNAString"

look more realistic to  align DNA sequences?
 
One more question.
 
What pairwise alignment tool would you recommend if I need to align a  
list#1 of 50-mer probes with a list#2 of more longer contigs (hundreds of  
bases):
 
I take each 50-mer probe from the list#1 and align it to each contig  from 
the list#2 
 
Finally, for each 50-mer probe I need to find the best match in some terms  
e.g. in terms of alignment scores.
 
I have tried pairwiseAlignment() but it works slowly and looks unfeasible  
for the list# 1 of 16798 probes vs. the list#2 of 14338 contigs, i.e. when  
output matrix should be 16798 by 14338.
 
I have looked at the mailing list and found suggestions to apply  
matchPattern/vmatchPattern but they provide the fact of a match for a  substring 
within a string rather than alignment score to compare  alignments.
 
Thanks
 
Best regards,
 
Alex
 
 
 
In a message dated 3/14/2011 9:04:04 A.M. Pacific Daylight Time,  
mtmorgan@fhcrc.org writes:

On  03/13/2011 06:58 PM, Alogmail2@aol.com wrote:
> 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"

Hi Alex --

here  'character' could be anything -- 'the quick brown fox',  whereas

>
> vs.
>
> pattern="DNAString",  subject="DNAString"

here pattern and subject are drawn from a  restricted alphabet and some 
symbols have particular meaning (e.g., 'N'  does not mean the nucleotide 
'N').

Martin

>
>  ?
>
> 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
>
>
>
>
>  ###############################
>
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> 119 Morgan Hall
> UC.Berkeley,CA  94720
>
>
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Computational Biology
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