[BioC] matchTable for pairwiseAlignment in Biostrings?
Valerie Obenchain
vobencha at fhcrc.org
Thu Aug 22 22:38:05 CEST 2013
Hi Brian,
I don't know of a function that creates such a table but I think you can
create this with the start() and end() accessors.
pat <- DNAStringSet(c("CACCAGCT", "TTCGCC", "CGGTC"))
sub <- DNAString("ACTTCACCAGCTGACCTCG")
res <- pairwiseAlignment(pat, sub)
> res
Global PairwiseAlignmentsSingleSubject (1 of 3)
pattern: [1] CACCAGCT
subject: [5] CACCAGCT
score: -48.14596
DataFrame(subjectStart=start(subject(res)),
subjectEnd=end(subject(res)),
patternStart=start(pattern(res)),
patternEnd=end(pattern(res)))
DataFrame with 3 rows and 4 columns
subjectStart subjectEnd patternStart patternEnd
<integer> <integer> <integer> <integer>
1 5 12 1 8
2 3 8 1 6
3 1 5 1 5
Valerie
On 08/21/2013 08:40 AM, Brian Herb wrote:
> Hi all,
>
> I feel like I'm missing some obvious function, but is there a simple way to
> output a table of matching start and end positions between the subject and
> pattern in a pairwiseAlignment result (say from a global-local alignment)?
> For example:
>
> s.pos1 s.pos2 p.pos1 p.pos2
> [1,] 354 359 1 6
> [2,] 360 364 9 19
>
> where s.pos1 and s.pos2 are the start and end of a section of the subject
> that corresponds to the start and end (p.pos1 and p.pos2) of the pattern,
> taking into account insertions and deletions. I know the insertion and
> deletion information is easily available, but I haven't found a function in
> the literature that that summarizes them into a mummer like output of
> corresponding start and end positions.
>
More information about the Bioconductor
mailing list