How to extract 3', 5' UTR sequences from genbank records using python, PERL and R code?

Question

[mathavanbioinfo]

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]

[hugo.avila]

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

[WouterDeCoster]

Please take a look at the biopython cookbook and tutorial.

Answer 1

[padwalmk]

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

Answer 2

[zubenel]

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.