NCBI protein IDs convert to gene IDs and then gene sequences
Hi everyone,
I have many NCBI Ref protein IDs (e.g. NP_051085.1), I need to convert them to gene IDs, and then extract gene sequences. I searched NCBI ftp website, but could not find proper links. So I need two dbs: one is Ref protein id vs Ref gene id, the other is Ref gene sequence fasta file.
Could anyone help to provide me a link or other method to achieve this? I will much appreciate your kind helps. THANKS.
1 answer
Hello,
here is an up-to-date solution:
This can be done quite easily with Ensembl's biomart. In your case got the biomart version for plants.
- in
DatasetchooseEnsembl Plants Genes 40 - in
FiltersopenGeneand selectInput external references ID list [Max 500 advised] - in the dropdown choose
RefSeq peptide ID(s)and paste in your ID(s) (one per line - in
Attributesclick the radio buttonSequencesand selectUnspliced (Gene)in theSequencesarea - click on
Resultsand you are done
fin swimmer
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I think you can directly use NCBI batch retrieve to retrieve your sequences when you have Protein ID's or accessions. Check here. Then you can download the sequences as fasta file from NCBI.
Hi Prakki, thanks for your help! However, I need to get the gene sequences instead of protein sequences. Need further helps. THANKS.
Oh. Ok then. Try using some converter like Biodbnet to convert to refseq nucleotide accession and try the batch retrieval. Some more ID converters are mentioned here also.
Hi Prakki, thanks a lot. Your comments are really helpful.