Which Sequences Should I Include In A Whole Genome Alignment Of Primates?

Question

[Ryan Thompson]

I'm looking into performing some whole-genome alignments of several nonhuman primate species, but I'm a little confused about which sequences I should include or exclude. Here is my current list of things I'm not sure about?

• Some of the species that I plan to align do not have mitochondrial or Y-chromosome assemblies available, while others do. Is this likely to cause problems, or can I ignore it?
• If I include both X and Y chromosomes, do I need to mask the pseudo-autosomal region in one or the other?
• What should I do with unlocalized sequences (e.g. "chr1_gl000191_random", "chrUn_gl000211")? What about the "hap" sequences (e.g. "chr6_apd_hap1")?

(No, not all my species are on UCSC, so I can't just use their alignments. If only.)

[aidan-budd]

What kinds of questions are you interested in addressing with the alignments?

[Ryan Thompson]

Mostly, mapping orthologous genes from well-annotated species (human, etc.) to my species of interest.

Answer 1

[Dan]

You could just look to see if you can get what you need here:

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

?

[Ryan Thompson]

No, my species isn't on there. However, I suppose I could look to see which sequences were included in those alignments and use them as examples.

[aidan-budd]

Sounds like a good idea