This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Getting Protein Information from NCBI Gene ID

Hi there,

So I have several excel files with 3000+ 'feature ID's' from next gen sequencing experiments. The feature ID's look as such:

LOC733603
MS4A7
CRISP3
RETN
TNFAIP6
ALPL
MMP8
IRG1
LTF
KCNJ15
HCRTR1

Basically, I would like to gather the following information about each of these features for Sus scrofa:

  • Gene name
  • Gene description
  • Protein Name
  • Amino acid sequence

I am using python, mainly the urllib2 package, to make HTTP requests to the NCBI gene database.

I can easily get the gene name and gene description by querying NCBI's gene database. I am then trying to use the associated gene ID to query either NCBI's protein database or uniprot but I am not sure what is the wiser approach? Has anyone else had the same scenario and have any useful advice or other ways about obtaining the data I am interested in?

Even easier, is there a way to access the NCBI related protein information with an NCBI gene ID?

Joey

protein ncbi-id ncbi python gene
• 5,565 views • link
updated by Ram Ram • written by joseph.orlando • joseph.orlando

3 answers

To obtain information corresponding to these gene symbols from UniProt, I recommend that you read this FAQ: http://www.uniprot.org/help/gene_symbol_mapping

Once you have your results, you can use the "Columns" button and customize your result table to include columns for gene and protein names and the amino acid sequence:

Query result in html view

Query result in tab-delimited format

Documentation about programmatic access to UniProt

• 0 views • link
updated by Ram Ram • written by Elisabeth Gasteiger Elisabeth Gasteiger

Apart from the above suggestion, you could use Batch Entrez which could provide links for the ids that you upload: http://www.ncbi.nlm.nih.gov/sites/batchentrez

• 0 views • link
updated by Ram Ram • written by Prash • Prash

Yet another suggestion would be to approach the mapping via Ensembl pig http://www.ensembl.org/Sus_scrofa/Info/Annotation

• 0 views • link
updated by Ram Ram • written by cdsouthan cdsouthan

Log in to answer this question.

More posts like this