Question: How to extract 3', 5' UTR sequences from genbank records using python, PERL and R code?
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gravatar for mathavanbioinfo
3 months ago by
India
mathavanbioinfo50 wrote:

Hello All, I have 1000 sequences of genebank records, I want to extract the only 3'UTR, 5'UTR sequences from the sequences and to store in excel format. Share your ideas and suggestion [using PERL or Python or R codes]

utr • 206 views
ADD COMMENTlink modified 3 months ago by zubenel70 • written 3 months ago by mathavanbioinfo50

Hi, please post a sample gbk file and define the headers that you want to see in your output file (Ex: seqID, locusTag, sequence ... ).

ADD REPLYlink written 3 months ago by hugo.avila10

Please take a look at the biopython cookbook and tutorial.

ADD REPLYlink written 3 months ago by WouterDeCoster43k
0
gravatar for padwalmk
3 months ago by
padwalmk80
padwalmk80 wrote:

Hi, It's unclear wither you have the gff file with you or fasta.

You can look in to following post

Extract coordinates of upstream region up to closest coding region in R

ADD COMMENTlink modified 3 months ago • written 3 months ago by padwalmk80
0
gravatar for zubenel
3 months ago by
zubenel70
zubenel70 wrote:

If you have gff file you might try to use gff2fasta.pl with option -feature set as "five_prime_UTR" or "three_prime_UTR" or something like that. Also you may read how to get sequences of specific features with BioPerl.

ADD COMMENTlink modified 3 months ago • written 3 months ago by zubenel70
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