Genome annotation by RAST

Question

[norhanmahfouz]

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

Answer 1

[Sukhi Singh]

Are the output files from RAST .gbk's?

Then,

1. union from the EMBOSS suite will work, e.g. 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

[norhanmahfouz]

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!