Question: How Do I Get A Neandertal Sequence?
3
gravatar for Rvosa
9.6 years ago by
Rvosa570
Leiden, the Netherlands
Rvosa570 wrote:

Hi,

I thought this would be doable. I have a region in the human genome (chromosome number, start, stop, strand) and I know that Ensembl have aligned a consensus of the neandertal genomes against a human genome - how do I get the neandertal version for that region? Like, a FASTA file, say. The genome browser has me confused.

Thanks!

genome fasta human • 5.2k views
ADD COMMENTlink written 9.6 years ago by Rvosa570
4
gravatar for Treylathe
9.6 years ago by
Treylathe950
San Francisco
Treylathe950 wrote:

I know Ensembl has a neanderthal browser: http://projects.ensembl.org/neandertal/ (but I can't get it to work right now, so can't remember)

You could also try the UCSC browser (there are tracks under Neanderthal group). If you just want the sequences of neanderthal that align with a particular region in sapiens sapiens, you could use the Table browser, http://genome.ucsc.edu/cgi-bin/hgTables?command=start, choose neanderthal sequence and analysis group, neandertal seq track and the primary (1st table). Choose the region in the human genome you are interested in and download the neanderthal reads as sequence (the format is FASTA). Or you might be able to just pull down the 'coding difference track' information if that's all you want (H-C coding Diff).

Here is the explanation of the data there: http://genome.ucsc.edu/Neandertal/

ADD COMMENTlink modified 14 months ago by _r_am31k • written 9.6 years ago by Treylathe950
3
gravatar for David Quigley
9.6 years ago by
David Quigley11k
San Francisco
David Quigley11k wrote:

You can browse this using the UCSC genome browser; they have a Neandertal track. Each of the six neadertal samples is a separate track; e.g. see this section of Hras. If you only care about a defined region, you can pull Neandertal sequence by region off of the table browser. Sorry that this isn't an Ensembl answer, but I only speak UCSC. I'm not sure how to make this automatically emit FASTA consensus; the tracks I saw show either reads or variations from the reference; variations from the reference are probably sufficient.

ADD COMMENTlink written 9.6 years ago by David Quigley11k
1

Manual. I navigated the web site until I had the example query I wanted and then copied the browser URL bar. If you look at the URL you can see all of the relevant parameters. I don't know if that is documented or subject to change.

ADD REPLYlink written 9.6 years ago by David Quigley11k

@David, how do you generate the link like that to UCSC tables? Is that manual or can you somehow generate a link given the current selection in the page?

ADD REPLYlink written 9.6 years ago by brentp23k

thanks. For some reason, I never noticed the URL changing as I was browsing around.

ADD REPLYlink written 9.6 years ago by brentp23k
1
gravatar for Larry_Parnell
9.6 years ago by
Larry_Parnell16k
Boston, MA USA
Larry_Parnell16k wrote:

Remember, the quality of data for these ancient samples leads to sequencing errors. These errors are not SNPs or other genetic variants. In other cases where there are differences between the six sources that gave the consensus Neandertal seq, there are legitimate SNPs. We've done some work with human and Neandertal data to look at SNPs conserved or not and need to pay attention to the SNP calls from the sequencing group who generated these data.

ADD COMMENTlink written 9.6 years ago by Larry_Parnell16k
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