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I am not sure which project database to use UCSC or Ensembl for my asthma study about ADRB2 gene (Arg/Arg-16 genotype).

I am using the original Human Genome Project database at the moment. However, I think Ensembl may be better suited for me.

Which genome database is good for Asthma research for Single Nucleotide Polymorphism (SNP variations)? I am looking for something which has existing visualisation tools or one where you can easily write one yourself.

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    $\begingroup$ I don't understand what you're asking. Ensembl has subsections that let you look at a single genomes. The fact that the database has other genomes is irrelevant. What are you calling the "original Human Genome Project"? Do you mean UCSC? What kind of data do you want to visualize? $\endgroup$
    – terdon
    Commented May 4, 2014 at 13:55
  • $\begingroup$ I think it can be UCSC that was first out. Tools that give overview of the database and let me then focus on some sample. $\endgroup$
    – Léo Léopold Hertz 준영
    Commented May 4, 2014 at 14:55
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    $\begingroup$ There is actually no difference between the databases, as they use the same datasets. Only the way you can display and look at the data is different. I like Ensembl more, but this is a flavour. And I got a pretty good introduction to it. $\endgroup$
    – Chris ♦
    Commented May 4, 2014 at 17:21
  • $\begingroup$ @Masi, all of them do that, that's the point og a genome browser. Can you please edit your question and narrow it down? I still don't know what you need that neither the UCSC nor Ensembl offer you. The only way to choose between them is personal choice or specific tools provided but since you don't explain what you want to do, it's hard to help. $\endgroup$
    – terdon
    Commented May 4, 2014 at 17:48
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    $\begingroup$ So you are looking for a way to find mapped SNPs in the ADRB2 gene? $\endgroup$
    – Chris ♦
    Commented May 5, 2014 at 8:44

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If you are looking for variations in a gene, there are a few databases you an consult.

You can of course use the usual genome browsers, search for your gene and then select the variations listed. For ADRB2 this looks like this on Ensembl. If you plan to retrieve and compare data from different genomes/genes, I really recommend learning how to use Biomart, as this is a very powerful tool.

Then you can use specific databases or search engines, which only target SNP's. Examples would be: DBSnp and SPSmart (which queries different databases).

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  • $\begingroup$ Very clear and excellent answer! Thank you for mentioning those tools! I am in the beginning of reviewing and learning them. :) $\endgroup$
    – Léo Léopold Hertz 준영
    Commented May 5, 2014 at 14:11
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    $\begingroup$ You're welcome. BTW: If you have the chance of participating in one of the Ensembl courses, do it. It is definitely worth the time. $\endgroup$
    – Chris ♦
    Commented May 5, 2014 at 14:43
  • $\begingroup$ I will do it when my studies go to Clinics phase. $\endgroup$
    – Léo Léopold Hertz 준영
    Commented May 5, 2014 at 18:20

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