I am not sure I can interpret the output of function "matchSeeds. I have run the on-line example myself: > data(hsSeqs) > data(s3utr) > hSeedReg = seedRegions(hsSeqs) > comphSeed = as.character(reverseComplement(RNAStringSet(hSeedReg))) > comph = RNA2DNA(comphSeed) > mx = matchSeeds(comph, s3utr) mx is a vector of lists: > is.vector(mx) [1] TRUE > length(mx) [1] 676 I would appreciate some help at understanding the results. For instance, I understand mx[1] is the list of matches for miRNA "hsa-let-7a". Each element of list mx[[1]] should be the list of target 3'utr sequances (??) to which the current miRNA 5' region match ??? For instance: > mx[1] $`hsa-let-7a` $`hsa-let-7a`$`1588` [1] 125 1107 $`hsa-let-7a`$`599` [1] 1240 $`hsa-let-7a`$`9180` [1] 757 $`hsa-let-7a`$`9180` [1] 757 I would like to understand what is the number apparing on the same line as the miRNA identifier, following the "$" sign. ($`1588`, $`599`, $`9180`;....) It must be an index into something ... But miRNA sequences are no more than 26 nucleotides long ... Does this coordinate mark the beginning of the matching region ? What about the following list of numbers ? For instance: [1] 125 1107 [1] 1240 [1] 757 Are these indices of 3'utr sequences ? Thank you in advance. Maura tutti i telefonini TIM! [[alternative HTML version deleted]]

Hi, On Aug 10, 2009, at 9:10 AM, <mauede at="" alice.it=""> <mauede at="" alice.it=""> wrote: > I am not sure I can interpret the output of function "matchSeeds. I > have run the on-line example myself: > >> data(hsSeqs) >> data(s3utr) >> hSeedReg = seedRegions(hsSeqs) >> comphSeed = as.character(reverseComplement(RNAStringSet(hSeedReg))) >> comph = RNA2DNA(comphSeed) >> mx = matchSeeds(comph, s3utr) > > mx is a vector of lists: > >> is.vector(mx) > [1] TRUE >> length(mx) > [1] 676 I think you mean a list of vectors (as a vector of lists isn't really possible). Call "is.list(mx)" -- you should get TRUE. Aslo, the documentation on the function says its value is: """A list containing one entry for each element of seeds that had at least one match in one entry of seqs. Each element of this list is a named vector containing the elements of seqs that the corresponding seed has an exact match in.""" > I would appreciate some help at understanding the results. > For instance, I understand mx[1] is the list of matches for miRNA > "hsa-let-7a". > Each element of list mx[[1]] should be the list of target 3'utr > sequances (??) to which > the current miRNA 5' region match ??? For instance: > >> mx[1] > $`hsa-let-7a` > $`hsa-let-7a`$`1588` > [1] 125 1107 > > $`hsa-let-7a`$`599` > [1] 1240 > > $`hsa-let-7a`$`9180` > [1] 757 > > $`hsa-let-7a`$`9180` > [1] 757 > > I would like to understand what is the number apparing on the same > line as the miRNA identifier, following the "$" sign. > ($`1588`, $`599`, $`9180`;....) > It must be an index into something ... But miRNA sequences are no > more than 26 nucleotides long ... Actually, I think 21 nt is what people are classifying as miRNA's these days. Smaller RNA's that are slightly larger/smaller than that are classified as other things (piRNA's, etc.) Sometimes it helps to ask yourself how you would design such a function, and what information actually would be useful for the function to return to the user. So, I bet that: if you call the function like so: mx = matchSeeds(comph, s3utr) A return value of: $`hsa-let-7a`$`1588` [1] 125 1107 Means that hsa-let-7a has two match in the 1588th sequence in s3utr. These matches probably start at positions 125 and 1107 on the 1588th sequence in said UTR. > Does this coordinate mark the beginning of the matching region ? > What about the following list of numbers ? For instance: > [1] 125 1107 > [1] 1240 > [1] 757 > Are these indices of 3'utr sequences ? It looks like you are on the right smoke trail, but why not just finish finding the fire would you want to take anybody's word for it? Not to sound rude, but these are questions you can easily answer yourself by playing around in your workspace to see if your intuition is correct: just look at the sequence of your 1588th UTR from 125 to 125+21 and see if the output makes sense. -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact