Getting Human Chimpanzee Divergent Sites

Question

[Philippe]

Hello everybody,

I want to analyse the divergent sites between human and chimpanzee genomes. As this has been extensively studied I was expecting to easily find this information in biological databases such as UCSC genome browser or Ensembl.

I found a UCSC table called ChimpSimpleDiff but it seems it has been computed only for old human genome assemblies and I could not find a way to download this table (I could then lift it up to the hg19 assembly for example).

I read in some publications that this dataset could also be retrieved via Ensembl Compara. However I could not find it through the Ensembl website, Biomart or the Ensembl mysql server (database Compara).

Do you know where this dataset could be found/downloaded? I prefer, if possible, to get it from relatively known databases as the ones previously cited as their content is more scrutinized and "mainstream". It is also easier to get than having to ask directly to a group who used such a dataset several years ago. =)

Thanks for your help.

Philippe.

Answer 1

[Pierre Lindenbaum]

I'm note sure if it fulfills your needs but there is a hg19 vs Chimp section in http://hgdownload.cse.ucsc.edu/goldenPath/hg19/vsPanTro3/

[Philippe]

Thanks but it does not seem I can make use of such data, at least not directly. If there is nothing preprocessed I could consider trying to extract information from those alignments.