NCBI protein IDs convert to gene IDs and then gene sequences

Question

[biolab]

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.

[Prakki Rama]

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.

[biolab]

Hi Prakki, thanks for your help! However, I need to get the gene sequences instead of protein sequences. Need further helps. THANKS.

[Prakki Rama]

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.

[biolab]

Hi Prakki, thanks a lot. Your comments are really helpful.

Answer 1

[finswimmer]

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 Dataset choose Ensembl Plants Genes 40
• in Filters open Gene and select Input 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 Attributes click the radio button Sequences and select Unspliced (Gene) in the Sequences area
• click on Results and you are done

fin swimmer