[BioC] Biostrings - pairwiseAlignment trimmed pattern returned

[Erik Wright]

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