Hi Seth, Is there any annotation packages mapping different types of gene identifiers, for example from gene symbol to Refseq, unigene to refseq, or other combination? I think they are really useful in the practice. Currently, we have to use some websites to do batch retrieve, which is not convenient. Actually, when using AnnBuilder to build annotation packages, all of these information has been retrieved. So why not build a package for each common organism? Thanks! Pan
[Bioc-devel] About annotation package mapping different types of gene identifiers
2 messages · Pan Du, Nianhua Li
Pan Du wrote:
Hi Seth, Is there any annotation packages mapping different types of gene identifiers, for example from gene symbol to Refseq, unigene to refseq, or other combination? I think they are really useful in the practice. Currently, we have to use some websites to do batch retrieve, which is not convenient. Actually, when using AnnBuilder to build annotation packages, all of these information has been retrieved. So why not build a package for each common organism? Thanks! Pan
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Hi, Pan, We already have some in the LLMappings packages (e.g. humanLLMappings). But they only provide GenBank accessions, go, UniGene and PubMed mappings to Entrez Gene. We will provide three new SQLite-based annotation packages in the next release (in a month), for human, mouse and rat, respectively. Their structure will be similar to affymetrix gene chip annotation packages such as hgu95av2, but the index will be Entrez Gene ID instead of probeset ID. Stay tuned... best nianhua