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!
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written
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biolab
4 answers
Readseq reads and writes sequences in various formats, including GenBank and GFF.
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.
You could try GFF-tools.
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written
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kangyueapril
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.
FYI this tool can't be found anymore, whether via the link above or below.
genbank2gff3.pl does the magic! http://www.hpa-bioinformatics.org.uk/biosnippets/snippets/115
Here is the canonical URL for this script: https://github.com/bioperl/bioperl-live/blob/master/scripts/Bio-DB-GFF/bp_genbank2gff3.pl.
Updated version of the "canonical" URL https://github.com/bioperl/bioperl-live/blob/master/bin/bp_genbank2gff3
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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bp_genbank2gff3.plhas many BioPerl dependencies because it is part of BioPerl. If you use Debian or Ubuntu,sudo apt install bioperland voilà, you have the tool in/usr/bin/bp_genbank2gff.This made my day, 6 years later.
Do you know if I can convert gbk files to BAM files?
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).