Question: Help with whole genome alignment
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gravatar for Alec Watanabe
3 months ago by
Alec Watanabe30 wrote:

Hello. I am looking for a tool or a methodology to make whole genome alignments with 50+ genomes. I used to use Gegenees that basically construct a matrix (heatmap) of similarity based on all vs all BLAST results. Recently, Gegenees stopped working and I don't know the reason. It might be because I've updated my Java version. It prints out some errors related to eclipse (which I don't know what it is). Anyways, is there any other tool or method similar to Gegenees? I need to know the similarity percentage between the organisms I am working with in order to define cut-off values for pan-genome analysis. Thank you!

tool help alignment • 208 views
ADD COMMENTlink modified 6 weeks ago by Biostar ♦♦ 20 • written 3 months ago by Alec Watanabe30

The only tools I know of that are capable of multiple whole genome alignments are LAST and Mauve, and even then, the alignments will be poor and take a long time. This is a largely unsolved problem in bioinformatics -the data is just too huge.

If you want to do all vs all pairwise alignments, you can use Wouter’s suggestion, or I believe mummer can do this fairly rapidly. Just bear in mind you’ll have at best, n choose k = 1225 alignments to do which is unlikely to be fast in any circumstances.

You might be able to use mash distances as a surrogate, though I’m not sure what the relationship between mash distances and ANI is (if any).

ADD REPLYlink modified 3 months ago • written 3 months ago by jrj.healey10k

Another tool which can do that is minimap2.

ADD REPLYlink written 3 months ago by WouterDeCoster36k

Thank you for all the answers. Just to provide a feedback, searching on the web I ended up finding about GET_HOMOLOGUES which can be used to create pan genome matrices thus fitting what I needed.

ADD REPLYlink written 3 months ago by Alec Watanabe30

Glad to hear you were able to move forward.

However (and for future reference), if GET_HOMOLOGUES has helped you doing so, I'm afraid your question was not really 'on topic' because 'whole genome alignments' is not something it will do. AFAIK it works on gene/protein level.

ADD REPLYlink written 6 weeks ago by lieven.sterck3.9k
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