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
_______________________________________________
BBB mailing list
[email protected]
http://www.bioinformatics.org/mailman/listinfo/bbb
