Question: Genome annotation by RAST
gravatar for norhanmahfouz
5.4 years ago by
norhanmahfouz0 wrote:


I have used RAST command line tools, namely find_rnas, call_genes and svr_assign_using_figfams for the annotation of my 50+ set of ordered contigs; the output files from this give the positions of genes and rnas as well as the respective functions, however, I would like to have a gbk file that I can use as an input for whole genome alignment using mauve or progressive mauve and be able to directly see the annotations on the alignment. 

In other words, how can I merge all this info into one .gbk file? 


next-gen • 3.0k views
ADD COMMENTlink modified 5.4 years ago • written 5.4 years ago by norhanmahfouz0

No, they're not ... 
I managed by writing a script using Biopython modules to create a .gbk file ( kind of what the guy from the "Creating Embl File Using Biopython - Genome Annotation" post recommended) with the required data!

ADD REPLYlink written 5.4 years ago by norhanmahfouz0
gravatar for Sukhdeep Singh
5.4 years ago by
Sukhdeep Singh10k wrote:

Are the output files from RAST .gbk's?

1) union from the EMBOSS suite will work, eg. 

$ union -sequence FileA.gbk -sformat genbank -outseq FileB.gbk -osformat genbank -feature Y -auto

2) From BioPerl


Source :

More pointers

Creating Embl File Using Biopython - Genome Annotation

ADD COMMENTlink written 5.4 years ago by Sukhdeep Singh10k
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