How To Do Multiple Whole Genomes Alignments?

Question

[Ning-Yi Shao]

The problem now I will solve is that: we have 3 species, such as A, B, C. All of them are primates and have reference genomes. And we hope to get highly accurate multiple alignments of the whole genomes for further study.

I found webpage of UCSC:

http://genomewiki.ucsc.edu/index.php/Whole_genome_alignment_howto

But it is based on the case of alignments of 2 species, and I know they have multiple genomes alignments but I don't find the method section to describe it.

I also find the multiple alignment softwares on wikipedia:

http://en.wikipedia.org/wiki/List_of_sequence_alignment_software

But so many softwares, which is the one I need? Which is the fastest and most accurate one?

Any suggestion is welcome, thank you!

Answer 1

[2184687-1231-83-]

If the three primate genomes you are interested in are in the list of publicly available primate genomes in UCSC/Ensembl/NCBI, you could just use the pre-calculated multiple whole-genome alignments in Ensembl Comparative Genomics:

http://www.ensembl.org/info/docs/compara/analyses.html

The current version is a 6-way primate whole-genome alignments set:

6 primates EPO (method_link_type="EPO" : species_set_name="primates") Human (Homo sapiens) Chimpanzee (Pan troglodytes) Gorilla (Gorilla gorilla) Pongo abelii Macaque (Macaca mulatta) Marmoset (Callithrix jacchus)

They can be downloaded from the ftp site here:

ftp://ftp.ensembl.org/pub/current_emf/ensembl-compara/epo_6_primate/

[Ning-Yi Shao]

Thank you!

But I need only three primates alignment. Is it possible to find a more detail description of the method to do the alignments? I hope to get exact whole genome alignments of Hg19, panTro3, and rheMac2.

[Ning-Yi Shao]

Now I am checking EPO pipeline, would you mind to give me more hint of the pipeline? For example, should I remove all repeat regions? Thank you very much!

Answer 2

[Treylathe]

If they are three species that are sequenced and complete, you can get an pre-computed alignment of specific regions of the species of choice from UCSC: http://screencast.com/t/JCb3UpsfvSf

I'd also check out Vista for pre-computed whole genome alignments. http://pipeline.lbl.gov/cgi-bin/gateway2

If the species you are looking for are incomplete or not included, or you'd like to do the alignment independently with different parameters, methodology, etc, Multiz is a good start. Vista can be used to add sequences too.

[Ning-Yi Shao]

Thank you very much! Now I am trying multiz and EPO pipeline.

Answer 3

[Joe Fass]

I've used Mauve (http://gel.ahabs.wisc.edu/mauve/) in the past. If you're aligning relatively complete assemblies, it might be what you're looking for. It also has a feature ("move contigs" or contig reordering) where it will rearrange contigs (from, say, a draft assembly) until they're in an order / orientations that maximize alignment with a trusted reference.