program to pull out 5'and 3'utr from cds file
0
0
Entering edit mode
6.2 years ago

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

cds utr program • 1.9k views
ADD COMMENT
0
Entering edit mode

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 REPLY
0
Entering edit mode

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 REPLY

Login before adding your answer.

Traffic: 1644 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6