Question: Mauve File Format
0
gravatar for trionanibrannacht
7 months ago by
trionanibrannacht0 wrote:

Hi everyone,

I recently downloaded mauve and I'm having trouble trying to upload GenBank files. I understand mauve only accepts GenBank files in .gbk format. However when I download my desired sequences from the ncbi website they are in .gb format. I've tried running the .gb files but I keep getting an error. Is there some way I could convert the files to .gbk?

Thanks for any replies in advance!

.gb mauve .gbk ncbi • 530 views
ADD COMMENTlink written 7 months ago by trionanibrannacht0
1

Can you post the exact error?

ADD REPLYlink written 7 months ago by genomax49k
1

Make sure you have Genbank (full) files, which contain the full sequence at the end of the file. Non “full” Genbanks just contain feature information and won’t work.

You’ll need to past the exact error for us to be able to help you much further.

ADD REPLYlink written 7 months ago by jrj.healey4.6k

Try renaming your files to .gbk. I remember having no problems to align complete genomes in NCBI genbank files and my draft fastas.

Which version of Mauve? What exactly are you trying to do?

ADD REPLYlink written 7 months ago by h.mon15k

I've tried to rename the files but unfortunately, this is not working.

I'm using Mauve 20150226 which I downloaded from here http://darlinglab.org/mauve/download.html. I'm trying to align two strains of synechcocystis to detect SNP's and I was hoping using GenBank files would provide more context to the alignment than fasta.

ADD REPLYlink written 7 months ago by trionanibrannacht0
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