Dear all,
I am learning how to "Finding Candidate Binding Sites for Known 
Transcription Factors via Sequence Matching" from the Bioconductor 
online help file at 
http://www.bioconductor.org/help/workflows/gene-regulation-tfbs/

When I ran the following codes, I can not match the results back to the 
UCSC genome browser results.

||>|orfs <- as.character(mget("RHOA", org.Hs.egSYMBOL2EG))
||||>||  pfm.grhl <- query(MotifDb,"GRHL")[[1]]
> pcm.grhl <- round(100 * pfm.grhl)
> chromosomal.loc <-  transcriptsBy(TxDb.Hsapiens.UCSC.hg19.knownGene, by="gene") [orfs]
> promoter.seqs <-  getPromoterSeq(chromosomal.loc, Hsapiens, upstream=1000, downstream=0)
> promoter.seqs <- unlist(promoter.seqs)
> matchPWM(pcm.grhl, promoter.seqs[[1]], "80%")
  Views on a 1000-letter DNAString subject
subject: AGCCCAGGTCAGGTTAGAGACCACTGGTATTGTT...GGCACTCGGAGGCGCGCACGTCGTTCCCCGCCCT
views:
     start end width
[1]   347 354     8 [AAGCCTCA]

> chromosomal.loc
GRangesList of length 1:
$387
GRanges with 2 ranges and 2 metadata columns:
       seqnames               ranges strand |     tx_id     tx_name
          <Rle>            <IRanges>  <Rle> | <integer> <character>
   [1]     chr3 [49396579, 49449428]      - |     15517  uc010hku.3
   [2]     chr3 [49396579, 49449526]      - |     15518  uc003cwu.3

---
seqlengths:
                   chr1                  chr2 ...        chrUn_gl000249
              249250621             243199373 ...                 38502

As|||49396579-1000+347=49395926, I use it as an absolute position.|
However, when I visit the UCSC genome browser, for the region chr3:||||49395926||-||||49395934.||
  I got [GTGCTCCTC], instead of [|||AAGCCTCA] or similar.|

So, could anyone tell me how to calculate the absolute genome  position from the output of of function matchPWM ?.

Thanks in advance.

Holly
|



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