Question: Any tools converting Genbank format to GFF3 format?
5
gravatar for biolab
4.7 years ago by
biolab1.1k
biolab1.1k wrote:

Dear all,

As my title describe, I am asking help to convert Genbank format to GFF format.  By GOOGLing, I found a perl script bp_genbank2gff3.pl), which has many bioperl dependencies.  Could anyone inform me other easy-to-use tools?  Any suggestions will be appreciated.  THANKS a lot in advance!

genbank gff • 18k views
ADD COMMENTlink modified 3.1 years ago by sara.barbosa.salazar0 • written 4.7 years ago by biolab1.1k
2

bp_genbank2gff3.pl has many BioPerl dependencies because it is part of BioPerl. If you use Debian or Ubuntu, sudo apt install bioperl and voilà, you have the tool in /usr/bin/bp_genbank2gff.

ADD REPLYlink modified 3.2 years ago • written 3.2 years ago by Charles Plessy2.7k
5
gravatar for a.zielezinski
4.7 years ago by
a.zielezinski8.9k
a.zielezinski8.9k wrote:

Readseq reads and writes sequences in various formats, including GenBank and GFF.

ADD COMMENTlink written 4.7 years ago by a.zielezinski8.9k

Thank you, a.zielezinski, your answer is really helpful for me!

ADD REPLYlink modified 4.7 years ago • written 4.7 years ago by biolab1.1k

FYI this tool doesn't convert to GFF3 v3, but to v2. Moreover, its latest version seems to be from May 2010. Nevertheless, the source code is available.

ADD REPLYlink written 4.2 years ago by Timothée Flutre20
1
gravatar for kangyueapril
4.7 years ago by
kangyueapril80
United States
kangyueapril80 wrote:

You could try GFF tools. http://www.raetschlab.org/suppl/gff-tools

ADD COMMENTlink written 4.7 years ago by kangyueapril80

Hi Kangyueapril,

Thank you very much for your answer. I have one more question: I logged on the Glaxy site (https://galaxy.cbio.mskcc.org/), and found GenBank to GFF converter page, however, I was unable to find the link to download the tool.  Do you have any solution?  THANKS again.

ADD REPLYlink written 4.7 years ago by biolab1.1k
1

https://galaxy.cbio.mskcc.org/root?tool_id=fml_genbank2gff

ADD REPLYlink written 4.7 years ago by kangyueapril80

Thank you, Kangyueapril!

ADD REPLYlink written 4.7 years ago by biolab1.1k

FYI this tool can't be found anymore, whether via the link above or below.

ADD REPLYlink modified 4.2 years ago • written 4.2 years ago by Timothée Flutre20
0
gravatar for musta1234
3.2 years ago by
musta123410
musta123410 wrote:

genbank2gff3.pl does the magic! http://www.hpa-bioinformatics.org.uk/biosnippets/snippets/115

ADD COMMENTlink written 3.2 years ago by musta123410
2

Here is the canonical URL for this script: https://github.com/bioperl/bioperl-live/blob/master/scripts/Bio-DB-GFF/bp_genbank2gff3.pl.

ADD REPLYlink modified 3.2 years ago • written 3.2 years ago by Charles Plessy2.7k
0
gravatar for sara.barbosa.salazar
3.1 years ago by
sara.barbosa.salazar0 wrote:

Do you know if I can convert gbk files to BAM files?

ADD COMMENTlink written 3.1 years ago by sara.barbosa.salazar0
1

If that's something you truly wonder about I suggest you do some reading about what those files are, which data they contain and how they are obtained/made, because you absolutely can't convert genbank format (gbk) in binary Sequence Alignment/Map files (BAM).

ADD REPLYlink written 3.1 years ago by WouterDeCoster42k
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