Which genome browser to display bacterial draft genomes?

Question

[dago]

Maybe this is a naive question, but I did manage to find a way around it so far.

I open without problems the complete .gbk file of few bacteria genomes I am working with in Artemis or IGV. However, I was quite surprised to realize that when I try to load the .gbk for draft genomes, only one contig is loaded.

Do you have any idea how could I display all the contigs? Are there any special option/programs to consider when dealing with draft (multi contigs) genomes?

[Neilfws]

Can you link to a .gbk file which has this problem?

[dago]

@Neilfws thanks for the reply. Basically, for all the draft genomes I am working with I have the same problem. when multiple contigs are in the .gbk I can always display just one.

[Neilfws]

Would still help to provide an example if you want other people to troubleshoot this.

[dago]

Well, you are right but to check that it is simply necessary to download any bacterial genome that has multiple contigs on NCBI (e.g. this Salmonella strain). The curious thing is that when I try to upload a .gff file in Artemis all the contigs are read. Am I missing something concerning the file formats?

Answer 1

[Ann]

Hello,

If you would like to give Integrated Genome Browser (IGB) a try, let us know. A lot of people are using IGB to visualize new bacterial genomes, and it seems to be a great use of the software.

If you would like some assistance with this, please get in touch. You could help us double-check that we are doing a good job of of supporting the .gbk format.

Best way to get in touch is to email me directly at [e-mail]. Or you can visit http://www.bioviz.org/igb and click the "Contact" link.

Best of luck in your research!

Ann Loraine

[dago]

I am currently trying IGB. It looks really useful. However, when I try to "Open genome from file" I cannot select .gbk files. I am only allowed to open .fasta and similar other type of file. Any suggestion?

Answer 2

[dbarrios]

Another option is D3 Genome Browser, it works fine for bacteria .gbk files with multiple contigs.

It is a multi-platform software for quick and in-browser visualization of genomic data and it is available as an R package, a Python module and a WordPress plugin.

You can download it from CRAN, PyPI and the Website: http://d3gb.usal.es

Answer 3

[gaurav.singh]

Did you check with UCSC Genome Browser?

[dago]

I do not knwo this browser so much. Is there an avalible version for Ubuntu?