How Do I Get A Neandertal Sequence?
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13.0 years ago
Rvosa ▴ 580

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!

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13.0 years ago
Treylathe ▴ 950

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/

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13.0 years ago

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.

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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.

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@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?

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

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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.

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