Entrez direct E-utilities - "efetch" command to retrieve CDS with protein accessions does not work
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7.8 years ago
al-ash ▴ 200

UPDATE: problem solved - it was just a typo and following line does what it is supposed to:

efetch -db protein -format fasta_cds_na -id XP_003399879.1

ORIGINAL REQUEST: I'm using Entrez Direct E-utilities to retrieve protein sequences with protein IDs but the option to retrieve CDS when using a protein ID is not working for me with the following command with an example protein accession:

efetch -db protein -format fasta_cd_na -id XP_003399879.1

although the command to fetch the protein FASTA works:

efetch -db protein -format fasta -id XP_003399879.1

Could you point me towards a mistake? Or is it because the efetch command does not work this way? Thanks!

Entrez Direct E-utilities efetch CDS retrieve • 8.5k views
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curious, what kind of ID is that?

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5.7 years ago
h.mon 35k

The problem is you have a typo in your command to recover CDS, is should be -format fasta_cds_na, not -format fasta_cd_na. The following works.

efetch -db protein -format fasta_cds_na -id XP_003399879.1
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7.8 years ago
DCGenomics ▴ 330

The following EDirect commands will get the CDS FASTA from a protein accession:

elink -db protein -id XP_003399879.1 -target nuccore | \
  efilter -molecule mrna | \
  efetch -format fasta_cds_na
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This solution doesn't work for me, it returns:

QueryKey value not found in filter input

QueryKey value not found in fetch input

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7.8 years ago
piet ★ 1.8k

The coding sequence (CDS) is a genomic nucleotide sequence, thus you have to retrieve it from the 'nucleotide' database rather then from the 'protein' database. In this case, XP_003399879.1, the coding sequence is XM_003399831.2:24..1547.

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In other words, it is not possible to use efetch with a protein ID as an input to obtain directly the CDS sequence, right? Rather, it is still necessary to convert first the protein ID to gene ID...I'm a bit surprised that the tool can not do this job...anyway, thanks for your reply!

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