Question: Which Sequences Should I Include In A Whole Genome Alignment Of Primates?
3
gravatar for Ryan Thompson
7.9 years ago by
Ryan Thompson3.4k
TSRI, La Jolla, CA
Ryan Thompson3.4k wrote:

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.)

genome alignment • 2.0k views
ADD COMMENTlink modified 7.9 years ago by Dan520 • written 7.9 years ago by Ryan Thompson3.4k
1

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

ADD REPLYlink written 7.9 years ago by aidan-budd1.9k

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

ADD REPLYlink written 7.9 years ago by Ryan Thompson3.4k
4
gravatar for Dan
7.9 years ago by
Dan520
Cambridge
Dan520 wrote:

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

?

ADD COMMENTlink written 7.9 years ago by Dan520
1

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.

ADD REPLYlink written 7.9 years ago by Ryan Thompson3.4k

Sounds like a good idea

ADD REPLYlink written 7.9 years ago by aidan-budd1.9k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2127 users visited in the last hour
_