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Search for multiple Patterns in Sequences

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 sequence bioconductor
• 2,136 views • link
updated by Ram Ram • written by bn • bn

1 answer

please see ?matchPDict

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updated by Ram Ram • written by Michael Dondrup Michael Dondrup

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.

• 0 views • link
updated by Ram Ram • written by bn • bn

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