Thanks Valerie,

Your explanation was much better than the one I found in the ?pairwiseAlignment man page.  It states:
"global" = align whole strings with end gap penalties ... "global-local" = align whole strings in pattern with consecutive subsequence of subject

Obviously the "whole strings" were not aligned in my previous email's examples.  A quick workaround for this issue that does not require changing the default gap penalties is to pad the subject sequences with multiple gaps on both ends.

pairwiseAlignment("ACTGACTGACTGACTG","--CTGAGAGGGTGATCGGCCACATTGGG--",type="global-local")
Global-Local PairwiseAlignedFixedSubject (1 of 1)
pattern: [1] ACTGACTGACTGACTG 
subject: [2] -CTGAGAGGGTGATCG 
score: -21.21098 

Thanks again,
Erik


On Feb 20, 2012, at 11:53 PM, Valerie Obenchain wrote:

> Hi Erik,
> 
> This behavior can be explained by altering the gapOpening and
> gapExtension arguments. You may want to look up "affine gap penalty" and
> look at paper referenced on the ?pairwiseAlignment man page.
> 
> By default gapOpening=-10 and gapExtension=-2. Using the defaults we
> match your example below,
> 
>    pairwiseAlignment("ACTGACTGACTGACTG", "AAGAAGAGTTATGGGAGTAACTGACC",
> gapOpening=-10, gapExtension=-2)
> 
> If we don't penalize the presence or extension of gaps we get an
> alignment that includes enough gaps to match the sequences. It is not
> recommended to not penalize gaps, this is for the sake of example.
> 
>    pairwiseAlignment("ACTGACTGACTGACTG", "AAGAAGAGTTATGGGAGTAACTGACC",
> gapOpening=0, gapExtension=0)
> 
> 
> The same can be done with your global-local example to get an idea of
> how these parameters affect the outcome. Additionally, global-local
> tries to find an alignment that matches the start and the end of one or
> the other sequence. This is useful for the case where one sequence is
> downstream of the other and they partially overlap. The global algorithm
> tries to align every residue in each sequence. You'll want to choose the
> algorithm that is most appropriate for your data then modify the
> arguments if necessary.
> 
> 
> Valerie
> 
> 
> 
> On 02/15/2012 02:25 PM, Erik Wright wrote:
>> Hello,
>> 
>> I have been using the Biostrings function "pairwiseAlignment" lately to perform sequence alignments.  I have discovered that with difficult alignments it sometimes returns incomplete patterns.  For example:
>> 
>> pairwiseAlignment("ACTGACTGACTGACTG","AAGAAGAGTTATGGGAGTAACTGACC")
>> Global PairwiseAlignedFixedSubject (1 of 1)
>> pattern: [1] ACT-----------GACTGACTGACT 
>> subject: [1] AAGAAGAGTTATGGGAGTAACTGACC 
>> score: -77.67886 
>> 
>> As you can see, the last character of the pattern ("G") has been removed.  If I set type="global-local" this does not happen, but it does in this instance:
>> 
>> pairwiseAlignment("ACTGACTGACTGACTG","CTGAGAGGGTGATCGGCCACATTGGG",type="global-local")
>> Global-Local PairwiseAlignedFixedSubject (1 of 1)
>> pattern: [2] CTGACTGACTGACTG 
>> subject: [1] CTGAGAGGGTGATCG 
>> score: -31.55991 
>> 
>> In this case the first character of the pattern ("A") was removed in the alignment.
>> 
>> Please help me to understand why this is happening, and if there might be a solution.
>> 
>> Thanks in advance,
>> Erik
>> 
>> 
>> sessionInfo()
>> R version 2.14.0 (2011-10-31)
>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>> 
>> locale:
>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>> 
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base     
>> 
>> other attached packages:
>> [1] RSQLite_0.10.0    DBI_0.2-5         Biostrings_2.22.0  IRanges_1.12.2   
>> 
>> loaded via a namespace (and not attached):
>> [1] tools_2.14.0
>> 
>> _______________________________________________
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>> Bioconductor@r-project.org
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>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>> 
> 


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