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

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
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updated by zubenel zubenel • written by mathavanbioinfo mathavanbioinfo

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

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written by hugo.avila hugo.avila

Please take a look at the biopython cookbook and tutorial.

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written by WouterDeCoster WouterDeCoster

2 answers

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

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written by padwalmk padwalmk

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.

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written by zubenel zubenel

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