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  • Get loop sequence from miRBase

    Does anyone know a way to extract the loop sequence from the miRNA hairpin. Basically I need to extract the part that is between the 3p- and 5p part of the hairpin.

  • #2
    Just align the 5p and 3p sequences to the hairpin sequence and take the bit between them.

    Comment


    • #3
      Originally posted by dpryan View Post
      Just align the 5p and 3p sequences to the hairpin sequence and take the bit between them.
      I have tried, but struggle to find a command that works.

      Comment


      • #4
        I would expect that either biopython or bioperl should make this relatively straight forward. The idea is to either use base python string matching or the pairwise2 module and global alignment.

        Comment


        • #5
          Here is another suggestion using R/Bioconductor. Good luck!

          Code:
          require(rtracklayer)
          require(BSgenome.Hsapiens.UCSC.hg19)
          require(ShortRead)
          
          mirTrack = import('ftp://mirbase.org/pub/mirbase/20/genomes/hsa.gff3')
          
          # split into hairpin, 5arm and 3arm
          hp = mirTrack[mirTrack$type != "miRNA"]
          arm5 = mirTrack[grepl("-5p", mirTrack$Name)]
          arm3 = mirTrack[grepl("-3p", mirTrack$Name)]
          
          # make key for matching hairpin with arm5 and arm3
          hp$arm5 = match(hp$ID, arm5$Derives_from)
          hp$arm3 = match(hp$ID, arm3$Derives_from)
          
          # discard hairpins lacking annotated 5p and 3p arms (loops not defined)
          hp = hp[!is.na(hp$arm3) & !is.na(hp$arm5)]
          
          # prepare 
          hp$loopStart = 0
          hp$loopEnd = 0
          
          # miRNAs on pos and neg strand have to be parsed separately
          ## posStrand
          isPos = as.vector(strand(hp) =="+")
          hp$loopStart[isPos] = end(arm5[hp$arm5[isPos]])
          hp$loopEnd[isPos] = start(arm3[hp$arm3[isPos]])
          
          ## negStrand
          hp$loopEnd[!isPos] = start(arm5[hp$arm5[!isPos]])
          hp$loopStart[!isPos] = end(arm3[hp$arm3[!isPos]])
          
          # GRanges for miRNA loops
          loops = GRanges(seqnames = seqnames(hp), 
            IRanges(hp$loopStart, hp$loopEnd),strand = strand(hp), 
            MI = hp$ID, Name = hp$Name)
          
          # sanity check
          hist(width(loops))
          
          # we don't want the first/last nt of bounding mature miRs
          loops = loops-1
          loops$seq = getSeq(Hsapiens, loops) 
          loops
          
          # export as fastaFile
          loopsFasta = loops$seq
          names(loopsFasta) = paste("loopSeq", loops$MI, loops$Name, sep = "_")
          writeFasta(loopsFasta, file = "mirbase20loops.fa")

          Comment


          • #6
            Hi! Here is a suggestion using R/Bioconductor. Good luck

            Code:
            require(rtracklayer)
            require(BSgenome.Hsapiens.UCSC.hg19)
            require(ShortRead)
            mirTrack = import('ftp://mirbase.org/pub/mirbase/20/genomes/hsa.gff3')
            
            # split into hairpin, 5arm and 3arm
            hp = mirTrack[mirTrack$type != "miRNA"]
            arm5 = mirTrack[grepl("-5p", mirTrack$Name)]
            arm3 = mirTrack[grepl("-3p", mirTrack$Name)]
            
            # make key for matching hairpin with arm5 and arm3
            hp$arm5 = match(hp$ID, arm5$Derives_from)
            hp$arm3 = match(hp$ID, arm3$Derives_from)
            
            # discard hairpins without annotated 5p and 3p arms
            hp = hp[!is.na(hp$arm3) & !is.na(hp$arm5)]
            
            # prepare
            hp$loopStart = 0
            hp$loopEnd = 0
            
            # miRNAs on pos and neg strand have to be parsed separately
            ## posStrand
            isPos = as.vector(strand(hp) =="+")
            hp$loopStart[isPos] = end(arm5[hp$arm5[isPos]])
            hp$loopEnd[isPos] = start(arm3[hp$arm3[isPos]])
            ## negStrand
            hp$loopEnd[!isPos] = start(arm5[hp$arm5[!isPos]])
            hp$loopStart[!isPos] = end(arm3[hp$arm3[!isPos]])
            # GRanges for miRNA loops
            loops = GRanges(seqnames = seqnames(hp),
            IRanges(hp$loopStart, hp$loopEnd),strand = strand(hp),
            MI = hp$ID, Name = hp$Name)
            # sanity check
            hist(width(loops), breaks = 50)
            # we dont want th efirst/last nt of bounding mature miRs
            loops = loops-1
            loops$seq = getSeq(Hsapiens, loops)
            # export
            loops
            loopsFasta = loops$seq
            names(loopsFasta) = paste("loop", loops$MI, loops$Name, sep = "_")
            writeFasta(loopsFasta, file = "mirbase20loops.fa")
            readLines("mirbase20loops.fa")

            Comment

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