How To Compare Complete Genomes With Mummer Or Other Tools

Question

[Layla]

Hi: I would like to replicate the results of the paper: Versatile and open software for comparing large genomes. In this paper the authors test the Mummer with complete genomes. The problem is when I compare the complete genomes of the A. nidulans and A. fumigatus. I know that when comparing those and because their closeness the results from the dotplot should be almost a perfect diagonal, but this does not happen. Anybody does know how to compare these genomes? Should I compare only chromosomes from both Fungi? From where do you actually recommend to download those genomes? Thanks

Answer 1

[Josh Herr]

Could you give us a little more information on the background of your question? Are you just replicating the study to understand how the authors did whole genome alignment using MUMMER or are you planning on aligning other genomes and just want practice first? You didn't provide a copy of your code or dotplot so we can't figure out what went wrong with your alignments.

The Kurtz et al paper from 2004 that you reference is a little old in my opinion and somewhat restrictive since I think MUMMER excels at pairwise alignment but may not be so optimal for whole genome alignment. I guess I can't really say that because I've personally never used it for whole genome alignments.

Here's a list of sequence alignment software.

When it comes to whole genome alignment, I prefer two genome alignment programs in particular. There are a few to choose from.

1. I like SyMAP best. If you are a windows user you will be out of luck as it only works on flavors of UNIX. You will also need some knowledge of MySQL. I have found that the program is relatively quick and accurate for whole genome alignments.

2. I would recommend MAUVE as a second choice. I think the output is a little cumbersome, but it works well.

As far as your sequences go, I would use Aspergillus fumigatus Af293, but there are numerous ones to download, and I would use the Aspergillus Comparative Database at the Broad Institute to download Aspergillus nidulans (and others). I would make sure your data is in a single FASTA file (I would use all the chromosomes, but it's your choice) and then you can use your annotation in GFF format. Both SyMAP and MAUVE can use GFF files in addition to FASTA data. It's up to you if you want to incorporate plastid data with your chromosomes. You can read the manuals and figure out how to use the programs and how to manipulate your text files as inputs.

JGI's Fungal Genomics Program also has a list of Aspergillus species for you to download.

[Layla]

Thanks for your help, in the page that you told me http://www.broadinstitute.org/annotation/genome/aspergillus_group/MultiDownloads.html which of all the files gives me the complete genome? it is the one that it says Gene downloads, genes.fasta?

[Josh Herr]

You're probably looking for the supercontigs, because that is as close to whole chromosomes as you are going to get. It all depends on your end goal of this exercise.

Perhaps before you embark on whole genome alignments, you should figure out what exactly you want to do, then you can start to plan each step of the analysis -- know what data you will need and what you want to do with it.