Thank you Hervé  . so if I want to determine to determine number of local
alignments between two strings no less than length 4, is that possible in
biostrings?
The alternative is create sliding window fragments  from one sequence and
use matchPattern ?

  subject1: TTAAACGTAAAATGAATAAGCCT
  subject:2 GGAAACGTGAATTGAATAAGCG




On Tue, Mar 25, 2014 at 1:06 PM, Hervé Pagès <hpages@fhcrc.org> wrote:

> Hi Al,
>
>
> On 03/25/2014 09:31 AM, Alpesh Querer wrote:
>
>> Hello,
>>
>> I understand the pairwiseAlignment() returns the (first) best match only,
>> is there a way for it to return all alignments for 2 sequences both local
>> and global?
>>
>
> Short answer is no.
>
> Long answer: I'm not sure what you'd like to get in case of a global
> alignment ("global" is short for "global-global").
> If you're doing "global-local" alignment, note that pairwiseAlignment()
> returns the *last* best match, not the first:
>
>   pattern <- DNAString("AAA")
>   subject <- DNAString("TTAAACGTAAAATGAAT")
>
> Then:
>
>   > pairwiseAlignment(pattern, subject, type="global-local")
>   Global-Local PairwiseAlignmentsSingleSubject (1 of 1)
>   pattern:  [1] AAA
>   subject: [10] AAA
>   score: 5.945268
>
> You can use matchPattern() to get all the matches that satisfy
> some criteria (but this criteria must be expressed in terms of
> edit distance):
>
>   > matchPattern(pattern, subject, max.mismatch=1, with.indels=TRUE)
>     Views on a 17-letter DNAString subject
>   subject: TTAAACGTAAAATGAAT
>   views:
>       start end width
>   [1]     3   5     3 [AAA]
>   [2]     9  11     3 [AAA]
>   [3]    10  12     3 [AAA]
>   [4]    15  16     2 [AA]
>
> This doesn't give you a score though nor does it guarantee that you'll
> get a match. However, if the returned Views object is not empty, then
> it's guaranteed to contain all the "best" matches. Even though the Views
> object can be post-processed to keep the best matches only, there is no
> way to ask matchPattern() something like "give me the best matches
> only".
>
> HTH,
> H.
>
>
>> Thanks,
>> Al
>>
>>         [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor@r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives: http://news.gmane.org/gmane.
>> science.biology.informatics.conductor
>>
>>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages@fhcrc.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>

	[[alternative HTML version deleted]]

