do you have any tools convert pdbid to accesion number of gene
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10.0 years ago
gbahramali ▴ 20

do you have any tools convert pdb-id to accession number of gene in ncbi (accession number)

gene • 3.1k views
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Newgene ▴ 370

You can also try MyGene.info service and its Python client. See the tutorial here.

out = mg.querymany(your_pdb_id_list, scopes='pdb', fields='entrezgene,go', species='human')

This will give you the matching ncbi gene ids and go accessions (or other annotations if you change fields parameter)

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thanks for your reply.it means that first download the phyton script and then??

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Could you please tell me how can I access to this site . I cannot understand the user guide

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Are you familiar with Python, R or any other programming language? If you give me your preference, I can provide more specific info.

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Thanks for your replying, I know C++ AND C SHARP language.

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I do step by step for install mygene. This step require install httplib2 (install using pip install httplib2) but unfortunately httplib2 is commercial and I cannot install it.

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I'm pretty sure httplib2 is not a commercial library. "pip install httplib2" should work if pip is working correctly in your environment. In fact, "pip install mygene" alone should be sufficient as it will install httplib2 automatically as dependencies.

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10.0 years ago
Bert Overduin ★ 3.7k

Please have a look at the Protein Identifier Cross-Reference Service (PICR) from EBI, which maps identifiers between many different databases, including NCBI RefSeq.

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thanks for your reply

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Thanks for your reply but didnot have accession number of GO(GENE ONTOLOGY)

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You didn't ask for GO accession numbers .... In that case, you can try Ensembl BioMart instead (provided your species of interest is part of Ensembl or Ensembl Genomes). You can find a BioMart tutorial on YouTube. Hope this helps.

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