do you have any tools convert pdb-id to accession number of gene in ncbi (accession number)
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gbahramali •
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)
thanks for your reply.it means that first download the phyton script and then??
Could you please tell me how can I access to this site . I cannot understand the user guide
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gbahramali •
Thanks for your replying, I know C++ AND C SHARP language.
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gbahramali •
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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gbahramali •
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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Bert Overduin
thanks for your reply
Thanks for your reply but didnot have accession number of GO(GENE ONTOLOGY)
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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