Question: Genome annotation by RAST
0
gravatar for norhanmahfouz
4.8 years ago by
Germany
norhanmahfouz0 wrote:

Hi,

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? 

Best,
Norhan

next-gen • 2.6k views
ADD COMMENTlink modified 4.8 years ago • written 4.8 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!
Thanks!

ADD REPLYlink written 4.8 years ago by norhanmahfouz0
0
gravatar for Sukhdeep Singh
4.8 years ago by
Sukhdeep Singh9.9k
Netherlands
Sukhdeep Singh9.9k wrote:

Are the output files from RAST .gbk's?
then,

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

Bio::SeqUtils->cat

Source : http://seqanswers.com/forums/showthread.php?t=7812

More pointers

http://seqanswers.com/forums/showthread.php?p=100585

Creating Embl File Using Biopython - Genome Annotation

ADD COMMENTlink written 4.8 years ago by Sukhdeep Singh9.9k
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