Getting nucleotide sequences using protein accession

Question

[bioinfo]

I have txt file with full of protein IDs, is there any way to get the nucleotide sequences (for genes) from NCBI or somewhere else using those protein IDs.

txt file

Q2FD83
B5LX01
P0AE06

[Pierre Lindenbaum]

Hello palc!

Questions similar to yours can already be found at:

• How To Programmatically Retrieve A Batch Of Fasta Sequences From For A List Of Uniprot Accession Ids?

We have closed your question to allow us to keep similar content in the same thread.

If you disagree with this please tell us why in a reply below. We'll be happy to talk about it.

Cheers!

PS: duplicate

[bioinfo]

Hi Pierre I'm interested to retrieve nucleotide sequences (!!!!) using uniprot ids. So it's not a duplicate. The other question deals with retrieving protein sequences.

[Pierre Lindenbaum]

ok: reopened

[bioinfo]

Didn't work..!! Please try once more..!!

Answer 1

[Elisabeth Gasteiger]

See also this thread: Getting Coding Strand (Cds) Using Uniprot Ids

And in particular my comment (from the UniProt helpdesk):

Getting Coding Strand (Cds) Using Uniprot Ids

I would like to point out that in the vast majority of cases, there is no single nucleic acid reference sequence for a given UniProtKB/Swiss-Prot protein sequence.

The canonical protein sequence is the outcome of thorough curation work, which often involves the merge of various sequences encoded by the same gene (in one species). In the annotation process, the most correct amino acid sequences are chosen and discrepancies are analyzed and documented.

cf this FAQ for more details: http://www.uniprot.org/faq/35

Answer 2

[5heikki]

http://www.uniprot.org/help/canonical_nucleotide

How do I get the nucleotide sequence that corresponds to the canonical UniProtKB sequence?

You cannot! ..

As you see, e.g. Q2FD83_ACIBA is linked to 13 nucleotide seqs.