[BiO BB] gff to sequence

Peter Rice pmr at ebi.ac.uk
Tue Oct 6 07:07:37 EDT 2009


On 03/10/09 01:29, Kie Kyon Huang wrote:
> Hi,
>
> Is there a way to quickly extract out the coordinates from a gff file
> and the corresponding sequence from a fasta file?

EMBOSS can do this. Sequences can be read from FASTA and feature tables
from GFF (gff2 or gff3)

extractfeat seqfile.fasta -ufo featfile.gff -out features.fasta

The output file (features.fasta) will have the sequences of all the
features with the positions and the feature type,
for example:

>X13776_8_24 [promoter] Pseudomonas aeruginosa amiC and amiR gene
ctggccgagcatctgct
>X13776_65_81 [promoter] Pseudomonas aeruginosa amiC and amiR gene
ctggcgagcctggagca
>X13776_121_126 [RBS] Pseudomonas aeruginosa amiC and amiR gene
aggaga


Hope this helps

Peter Rice




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