Entering edit mode
7.2 years ago
sv91707
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10
Hi all, Is there a way or tool to see all the mutations listed in ALL organisms or if not all, search singularly to see all "Mutations" and alleles in a particular region of a gene, or whole gene ?
I'm currently just using UCSC and Ensembl genome browser to see manually.
What exactly are you trying to answer with this? Without knowing more and if you already use the Ensembl Browser, why not use the Ensembl APIs (either the Variation Perl, if you know Perl, or the REST API) instead of doing it manually?
Or you can download the variation files from the FTP site of Ensembl. Keep in mind not every genome has got variation data. Check which one has got variation data in Ensembl.
Well, not all the variation but i forgot to mention, something like published mutations which are linked to diseases(Just in one specific gene). At the moment i'm looking everywhere like in OMIM for example or published literature. I just wanted to know if there is something not in my knowledge.
I see. If you are looking for mutations (or variants) associated with diseases, have a look at Open Targets. The data can be accessed programmatically but it's available for human genes and diseases only. You can explore our API documentation. You can get the evidence (based on Genetic association data for example) that was used to associated a gene with a disease e.g. BRAF in lung carcinoma (this is the view on the graphical user interface, our Platform. This is the REST API endpoint.
Variants curated from GWAS, UniProt and EVA are some of the data sources available in Open Targets and grouped in the Genetic association data type.
You can also get the somatic mutations, using this REST endpoint. Or the literature that has been mined for the co-occurrence of the terms BRAF and lung carcinoma in the same sentence of a research paper (literature as evidence for the association) Note that we work with the Experimental Factor Ontology (EFO) so that we represent the disease ontology with the parent and child diseases.
There is a Python client to access the REST API too, if you rather go down that route.