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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.
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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.Originally posted by dpryan View PostComment
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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
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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$Name, sep = "_") writeFasta(loopsFasta, file = "mirbase20loops.fa")Comment
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Hi! Here is a suggestion using R/Bioconductor. Good luck
Code:require(rtracklayer) require(BSgenome.Hsapiens.UCSC.hg19) require(ShortRead) mirTrack = import('ftp://mirbase.org/pub/mirbase/20/genomes/hsa.gff3') # split into hairpin, 5arm and 3arm hp = mirTrack[mirTrack$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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