Question: Whole Genome Alignment for plant genomes
0
gravatar for sbdk82
2.3 years ago by
sbdk8230
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 • 956 views
ADD COMMENTlink modified 2.3 years ago by microfuge950 • written 2.3 years ago by sbdk8230

Many people recommend Mauve or Mummer.

See also this link:

http://ensemblgenomes.org/info/data/whole_genome_alignment

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 2.3 years ago • written 2.3 years ago by natasha.sernova3.1k
0
gravatar for microfuge
2.3 years ago by
microfuge950
microfuge950 wrote:

Vista is quite a good tool specially geared towards WGD in plants. WGDs can be downloaded or computed http://pipeline.lbl.gov/downloads.shtml http://pipeline.lbl.gov/cgi-bin/gateway2

ADD COMMENTlink written 2.3 years ago by microfuge950
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