Question: Why the nucleotide sequences at each end of human chromosomes are "NNNNN..."
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gravatar for jinkuozhang
2.8 years ago by
jinkuozhang30
jinkuozhang30 wrote:

When I was fetching Human Genomics DNA sequence using Coordinates, I found that the nucleotide sequences at each end of human chromosomes(except chr17) are "NNNNN...". Could anyone tell me why they are "NNNN..." ranther than ATCG etc. Thanks!

> library(BSgenome.Hsapiens.UCSC.hg19)
> chrs = seqnames(Hsapiens)[1:24]
> chrs
[1] "chr1"  "chr2"  "chr3"  "chr4"  "chr5"  "chr6"  "chr7"  "chr8"  "chr9"  "chr10" "chr11"
[12] "chr12" "chr13" "chr14" "chr15" "chr16" "chr17" "chr18" "chr19" "chr20" "chr21" "chr22"
[23] "chrX"  "chrY" 
> first_10000_nt = getSeq(Hsapiens, names=chrs, start=rep(1, 24), end=rep(10000, 24))
> names(first_10000_nt) = chrs
> first_10000_nt
   A DNAStringSet instance of length 24
             width seq                                                          names
         [1] 10000 NNNNNNNNNNNNNNNNNNNNNNNNNNNNN...NNNNNNNNNNNNNNNNNNNNNNNNNNNN chr1
               ...   ... ...
        [24] 10000 NNNNNNNNNNNNNNNNNNNNNNNNNNNNN...NNNNNNNNNNNNNNNNNNNNNNNNNNNN chrY
> first_10000_nt["chr17"]
   A DNAStringSet instance of length 1enter code here
           width seq                                                           names
       [1] 10000 AAGCTTCTCACCCTGTTCCTGCATAGATA...CGCCATGTTGGCCAGGCTCTCTCGAACTC chr17
genome • 853 views
ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by jinkuozhang30
1
gravatar for Medhat
2.8 years ago by
Medhat8.4k
Texas
Medhat8.4k wrote:

Why Are There Ambiguous (N) Bases (Gaps) In The Human Genome

ADD COMMENTlink written 2.8 years ago by Medhat8.4k
2

More specifically: unresolved telomeric sequences.

ADD REPLYlink written 2.8 years ago by WouterDeCoster40k

Thank you! Medhat. Feel sorry for not searching the resolved question.

ADD REPLYlink written 2.8 years ago by jinkuozhang30
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