Question: Search for multiple Patterns in Sequences
1
gravatar for ad
4.6 years ago by
ad30
United States
ad30 wrote:

Hi, is there a way to use matchPattern from Biostrings to search for a set of patterns rather than just one? If not is there any similar alternative?

I'm using it this so far and it doesn't work

matchPattern("TAATTAAT|ATTAATTATAATAT|ATTATA",subSeq)

and

MotifSearch<-DNAStringSet(c("TAATTAAT","ATTAATTA","TAATAT","ATTATA"))
MotifResults<-vmatchPattern(MotifSearch,subSeq)

 

Could searching for multiple patterns in multiple strings work too?

 

thanks

pattern bioconductor sequence • 1000 views
ADD COMMENTlink modified 4.6 years ago by Michael Dondrup47k • written 4.6 years ago by ad30
0
gravatar for Michael Dondrup
4.6 years ago by
Bergen, Norway
Michael Dondrup47k wrote:

please see ?matchPDict

ADD COMMENTlink modified 6 months ago by RamRS27k • written 4.6 years ago by Michael Dondrup47k

Doesn't seem to work if the strings in the stringset are different sizes.

centralMotifSearch<-DNAStringSet(c("TAATTAAT","ATTAATTA","TAATAT","ATTATA"))
pCentralMotifSearch<-PDict(centralMotifSearch)
Error in .Call2("ACtree2_build", tb, pp_exclude, base_codes, nodebuf_ptr,  : 
  element 3 in Trusted Band has a different length than first element

Also matchPDict doesn't seem to work with an XStringSet.

ADD REPLYlink modified 6 months ago by RamRS27k • written 4.6 years ago by ad30
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