Question: How to convert Bed, or GFF3 files to fasta?
gravatar for ricfoz
12 months ago by
ricfoz0 wrote:

Hello everyone, i am new to the bioinformatic world, and i am trying to do a phylogeny with a gene. I am retrieving the sequences from different organisms, being some of those neandertal sequences, which i happen to download from a genome browser. These sequences are in GFF3 format, but i need to transform them to a .fasta file so i can run the phylogeny algorithm on them. Browsing through galaxy i have managed to convert them to BED format, i thought that could be an intermediate step in order to convert them to fasta, but i am stuck there.

Any suggestions on how to transform GFF3 files to fasta in galaxy?, thanks in advance and greetings to the community.

galaxy • 1.4k views
ADD COMMENTlink modified 12 months ago by Jennifer Hillman Jackson25k • written 12 months ago by ricfoz0
gravatar for Jennifer Hillman Jackson
12 months ago by
United States
Jennifer Hillman Jackson25k wrote:


Please see the tool: Extract Genomic DNA

The input is a BED/GTF/GFF dataset. The output is fasta sequence or interval format that includes the sequence.

A custom genome can be used whenever the target genome is not included on the server.

Thanks! Jen, Galaxy team

ADD COMMENTlink written 12 months ago by Jennifer Hillman Jackson25k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 170 users visited in the last hour