Question: program to pull out 5'and 3'utr from cds file
gravatar for vigneshprbh37
5.8 years ago by
vigneshprbh3730 wrote:

so i got nucleotide fasta sequence compiled for a set of genes iam working on, and i need to pull out 5' and 3'utrs from them .

before you ask i tried working with a source file containing entire database of utr, i was able to retrieve utr for around half of my geneset. many showed sequence being unavailable

from ncbi i was able to obtain the length of total gene sequence and cds and deduce the utr sequences

for eg gene x:   1..6521             cds : 455..4453

so 5'utr: 1-454     3'utr : 4454-6521.  iam going with this rationale

can you suggest a program to retrieve the set number of nucleotides for each gene

program utr cds • 1.8k views
ADD COMMENTlink written 5.8 years ago by vigneshprbh3730

If you have both files (a file with nucleotide sequences and a file with CDS localization) I could help you to write a script to extract UTR sequences for each gene.

ADD REPLYlink modified 5.8 years ago • written 5.8 years ago by a.zielezinski9.5k

Hi OP,

Any updates on your progress? I am also facing the same problems as you. Please let me know if you have found a solution to yours. 

I have tried the UCSC table browser. Apparently my species is only arbitrarily annotated with -/+ 200bp to the start/end codon as UTRs.

ADD REPLYlink written 5.7 years ago by wanziyi8960
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