Question: Whole Genome Alignment for plant genomes
gravatar for sbdk82
19 months ago by
United States
sbdk8230 wrote:

I am wondering if anyone recommend me better WGA tools available currently for aligning plant genomes. I am now using Mauve, Mummer and Mugsy. Are there any better tools available?

alignment wga • 597 views
ADD COMMENTlink modified 19 months ago by microfuge740 • written 19 months ago by sbdk8230

Many people recommend Mauve or Mummer.

See also this link:

they mention

"Two types of pairwise genome alignment are available in Ensembl Genomes, based on LastZ [1] (or its predecessor BlastZ [2]) and translated BLAT (tBLAT) [3]. LastZ is typically used for closely related species, and tBLAT for more distant species. The method of alignment affects the coverage of the genomes, with tBLAT expected to mostly find homologies in coding regions".

ADD REPLYlink modified 19 months ago • written 19 months ago by natasha.sernova2.9k
gravatar for microfuge
19 months ago by
microfuge740 wrote:

Vista is quite a good tool specially geared towards WGD in plants. WGDs can be downloaded or computed

ADD COMMENTlink written 19 months ago by microfuge740
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