Any tools converting Genbank format to GFF3 format?

Question

[biolab]

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!

[Charles Plessy]

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.

[Matteo Schiavinato]

This made my day, 6 years later.

[sara.barbosa.salazar]

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

[WouterDeCoster]

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).

Answer 1

[Andrzej Zielezinski]

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

[biolab]

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

[Timothée Flutre]

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.

Answer 2

[kangyueapril]

You could try GFF-tools.

[biolab]

Hi Kangyueapril,

Thank you very much for your answer. I have one more question: I logged on the Galaxy site, 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.

[kangyueapril]

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

[biolab]

Thank you, Kangyueapril!

[Timothée Flutre]

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

Answer 3

[musta1234]

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

[Charles Plessy]

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

[Flashton]

Updated version of the "canonical" URL https://github.com/bioperl/bioperl-live/blob/master/bin/bp_genbank2gff3

Answer 4

[maximilian]

Perl dependencies now make the canonical bioperl bp_genbank2gff3.pl tool more complicated to install with some common package managers such as miniconda.

Another python-based alternative is here in the biocode package.