Sequence id conversion & extraction

Question

[Pranavathiyani G]

How to convert the following IDs to GenBank nucleotide/gene ID & to retrieve nucleotide sequence in fasta format.

WP_003873519.1 WP_003892827.1 WP_003898538.1 WP_011739072.1 WP_023365853.1 WP_023366251.1 WP_023367098.1 WP_023369150.1 WP_023369156.1 WP_023369158.1 WP_023370844.1 WP_023370846.1 WP_023370878.1 WP_023370926.1 WP_023370928.1 WP_023370930.1 WP_023370920.1 WP_023370924.1 WP_023370932.1 WP_023370934.1 WP_023370951.1 WP_023370953.1 WP_023370955.1 WP_023370958.1 WP_023370962.1 WP_023370964.1 WP_023370966.1 WP_023370968.1 WP_023371064.1 WP_023371068.1 WP_023371072.1 WP_023371103.1 WP_023372313.1 WP_023372327.1 WP_023372450.1 WP_023373686.1 WP_023373729.1 WP_023373731.1 WP_023364557.1 WP_023369615.1 WP_023370856.1 WP_023371070.1 WP_023373127.1 WP_036395287.1

Answer 1

[Sej Modha]

To retrieve gene ID from the protein you can use following command

esearch -db protein -query "WP_003873519.1"|elink -target gene|efetch

Following command will give you all CDS and then you can extract WP_003873519.1from the all CDS fasta file.

esearch -db protein -query "WP_003873519.1"|elink -target gene|elink -target nuccore|efilter -query refseq|efetch -format  fasta_cds_na > output.fa

Answer 2

[GenoMax]

If you have access to the pre-formatted refseq_protein blast database then the easiest option is to use the blastdbcmd utility (part of blast+) to iterate over the ID's and get the sequence in fasta format like so:

$ blastdbcmd -db /path_to/refseq_protein -entry WP_023370932.1 -outfmt "%f"

You could also use -entry_batch option and provide a file with the ID's (one ID on each line).

$ blastdbcmd -db /path_to/refseq_protein -entry_batch file_w_ID -outfmt "%f"

Answer 3

[Sej Modha]

Are these protein IDs? Would you like to retrieve gene sequence or the protein sequence in fasta format?

[Pranavathiyani G]

These are Protein RefSeq ID. I want to retrieve gene sequences in fasta format.