Any tools converting Genbank format to GFF3 format?
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6.6 years ago
biolab ★ 1.3k

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!

gff genbank • 25k views
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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.

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

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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).

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6.6 years ago

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

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

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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.

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6.6 years ago
kangyueapril ▴ 80

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

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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.

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Thank you, Kangyueapril!

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

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5.0 years ago
musta1234 ▴ 20

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

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15 days ago
maximilian • 0

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.

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