NCBI Entrez Direct UNIX E-utilities

Post by: Sej Modha
April 20, 2016
4 Comments

I use NCBI Entrez Direct UNIX E-utilities regularly for sequence and data retrieval from NCBI. These UNIX utils can be combined with any UNIX commands.

It is available to download from the NCBI website: ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/

A few useful examples for NCBI edirect utilities.

Download a sequence in fasta format from NCBI using accession number

esearch -db nucleotide -query "NC_001552" | efetch -format fasta > output.fasta

Batch retrieval for all proteins for taxon ID. This example will download all proteins for viruses in fasta format.

esearch -db "protein" -query "txid10239[Organism]" | efetch -format fasta > output.fasta

Download sequences infasta format from NCBI using edirect using isolate info

esearch -db nucleotide -query "GDST008"|efetch -format fasta > output.fasta

Download sequences from NCBI using edirect using bioproject accession or ID

esearch -db bioproject -query "PRJNA285593" | elink -target nuccore|efetch -format fasta
esearch -db bioproject -query "285593[id]" | elink -target nuccore|efetch -format fasta

Get all CDS from a genome

esearch -db protein -query 302315370| elink -target nuccore|efetch -format ft| grep -A 4 --no-group-separator CDS
esearch -db protein -query 302315370 | elink -target nuccore|efetch -format fasta_cds_na| grep YP_003815423.1

Get taxonomy ID from protein accession number

esearch -db protein -query "NP_066243"| elink -target taxonomy |efetch -format uid
#use gi instead
esearch -db protein -query "10314000"| elink -target taxonomy |efetch -format uid

Get taxonomy ID from accession number using esummary

esearch -db nucleotide -query "NC_001552"|esummary|grep TaxId

Get full lineage from accession number
Tip : xtract can be used to fetch any element from the xml output

esearch -db protein -query "NP_066243"| elink -target taxonomy |efetch -format xml |xtract -element Lineage

Get scientific name from accession number

esearch -db protein -query "NP_066243"| elink -target taxonomy |efetch -format xml |xtract -element ScientificName|cut -f1

Download all refseq protein sequences for viruses

esearch -db "protein" -query "txid10239[Organism] AND refseq[filter]"|efetch -format fasta > refseq_protein_viruses.fa

Download reference genome sequence from taxonomy ID
Note: Using efilter command

esearch -db taxonomy -query "txid11053 [Organism]"|elink -target nuccore|efilter -query "refseq"|efetch -format fasta >output.fa

Get all proteins from a genome accession

elink -db nucleotide -id JN420361.1 -target protein|efetch -format DocSum
#Downloads protein sequences in fasta format
elink -db nucleotide -id JN420361.1 -target protein|efetch -format fasta
#Get GI for these protein
elink -db nucleotide -id JN420361.1 -target protein|efetch -format uid
#Retrieve accession numbers of the protein
elink -db nucleotide -id JN420361.1 -target protein|efetch -format acc

Extract genome accession from protein accession – DBSOURCE attribute in genbank file and an alternative to the script mentioned in one of my earlier blog post.
Note: Following command would work with protein accession and GIs used as -id parameter in elink command.

elink -db protein -id 817524604 -target nuccore|efetch -format acc
#Use protein accession instead of GI as -id
elink -db protein -id YP_009134732.1 -target nuccore|efetch -format acc

More info about NCBI Entrez Direct E-utillities is available on the NCBI website. http://www.ncbi.nlm.nih.gov/books/NBK179288/

Categories: eutils, UNIX