Extract 3'utr from annotation file

Question

[najibveto]

hello

i am looking to extract the 3'utr sequences of fathead minnow fish using the annotation file and the genome. http://www.ncbi.nlm.nih.gov/genome/?term=fathead%20minnow

can someone help me or advice me on the method to do it?

[iraun]

If UTR features are annotated in your annotation file, you can use bedtools getfasta utility to extract the sequences. You must provide the genome file and a BED/GFF/VCF file of ranges to extract (3'UTR in your case).

If UTR are not annotated yet, you'd need to annotate them using some ORF prediction tool ...

Answer 1

[Devon Ryan]

If the UTRs are unannotated, you might have luck with the GenomicFeatures package in R. UTRs would be the difference between exon and CDS entries per transcript (there are some functions that enable doing that, read through the vignette). If you're really luck then the txdb object that you create will already do this, but I've never tried.

The you can either write those to a file and use bedtools getfasta or use an equivalent method in R.