Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
GenBank to .tbl (Sequin format) ErinL Bioinformatics 21 01-15-2019 01:57 AM
convert gff to embl/genbank bio_informatics Bioinformatics 5 04-21-2014 05:20 PM
NCBI feature table (.tbl) format mike.t Bioinformatics 1 02-01-2014 06:53 PM
1. embl/gbk to FASTA conversion; 2. 16s RNA to be found in a embl/gbk file ashuchawla Bioinformatics 3 05-16-2012 07:00 AM
NCBI's format allo Bioinformatics 0 03-26-2012 07:26 PM

Thread Tools
Old 10-31-2014, 06:51 AM   #1
Junior Member
Location: southampton, UK

Join Date: Oct 2014
Posts: 8
Default .embl to NCBI .tbl format

i have an annotated genome in .embl format and would like to extract the feature table from this so i can use it for submission to NCBI via tbl2asn along with a genome fast file.
Does anyone know a way to parse feature tables from .embl files, i'm really stuck here.
The bacterium i am working on has no reference genome, so it has unfortunately fallen to me to submit one.
akp1d12 is offline   Reply With Quote
Old 11-01-2014, 04:02 AM   #2
Peter (Biopython etc)
Location: Dundee, Scotland, UK

Join Date: Jul 2009
Posts: 1,543

BioPerl, Biopython, EMBOSS etc all understand and can parse EMBL format, so could at least convert it into GenBank format from which you might have more options?
maubp is offline   Reply With Quote
Old 11-01-2014, 04:34 AM   #3
Senior Member
Location: East Coast USA

Join Date: Feb 2008
Posts: 7,076

Once you get to the GenBank format as Peter suggested this should help with remainder of the task:
GenoMax is offline   Reply With Quote

.embl, .tbl, feature table, ncbi, tbl2asn

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 02:06 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO