dear all:
pairwiseAlignment {Biostrings} can only output aligment result
if i need the number of mismatch or gap
how can i extract those information?
thank you
--
shan gao
Room 231(Dr.Fei lab)
Boyce Thompson Institute
Cornell University
Tower Road, Ithaca, NY 14853-1801
Office phone: 1-607-254-1267(day)
Official email:sg839 at cornell.edu
Facebook:http://www.facebook.com/profile.php?id=100001986532253
Hi,
On 04/26/2012 06:18 PM, wang peter wrote:
> dear all:
> pairwiseAlignment {Biostrings} can only output aligment result
> if i need the number of mismatch or gap
> how can i extract those information?
The Biostrings package has an entire vignette dedicated to
pairwiseAlignment() and related tools. How to extract this kind
of information is explained in details. For example:
> globalAlign
Global PairwiseAlignedFixedSubject (1 of 1)
pattern: [1] ACTTCACCAGCTCCCTGGCGGTAAGTTGATC---AAAGG---
AAACGCAAAGTTTTCAAG
subject: [1]
GTTTCACTACTTCCTTTCGGGTAAGTAAATATATAAATATATAAAAATATAATTTTCATC
score: -52
> nmatch(globalAlign)
[1] 33
> nmismatch(globalAlign)
[1] 21
> nindel(pattern(globalAlign))
Length WidthSum
[1,] 2 6
Cheers,
H.
>
> thank you
>
--
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 at fhcrc.org
Phone: (206) 667-5791
Fax: (206) 667-1319
On 04/27/2012 03:08 AM, Hervé Pagès wrote:
> Hi,
>
> On 04/26/2012 06:18 PM, wang peter wrote:
>> dear all:
>> pairwiseAlignment {Biostrings} can only output aligment result
>> if i need the number of mismatch or gap
>> how can i extract those information?
>
> The Biostrings package has an entire vignette dedicated to
Here's how you find vignettes for the version of Biostrings installed
on
your computer
> vignette(package="Biostrings") ## available vignettes
> vignette(package="Biostrings", "PairwiseAlignments") ## a vignette
Martin
> pairwiseAlignment() and related tools. How to extract this kind
> of information is explained in details. For example:
>
> > globalAlign
> Global PairwiseAlignedFixedSubject (1 of 1)
> pattern: [1] ACTTCACCAGCTCCCTGGCGGTAAGTTGATC---AAAGG---
AAACGCAAAGTTTTCAAG
> subject: [1]
GTTTCACTACTTCCTTTCGGGTAAGTAAATATATAAATATATAAAAATATAATTTTCATC
> score: -52
>
> > nmatch(globalAlign)
> [1] 33
>
> > nmismatch(globalAlign)
> [1] 21
>
> > nindel(pattern(globalAlign))
> Length WidthSum
> [1,] 2 6
>
> Cheers,
> H.
>
>>
>> thank you
>>
>
>
--
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
Location: M1-B861
Telephone: 206 667-2793
