Format Selection

  -format        Format of record or report
  -mode          text, xml, asn.1, json
  -style         master, conwithfeat

Direct Record Selection

  -db            Database name
  -id            Unique identifier or accession number
  -input         Read identifier(s) from file instead of stdin

Sequence Range

  -seq_start     First sequence position to retrieve
  -seq_stop      Last sequence position to retrieve
  -strand        1 = forward DNA strand, 2 = reverse complement
                   (otherwise strand minus is set if start > stop)
  -forward       Force strand 1
  -revcomp       Force strand 2

Gene Range

  -chr_start     Sequence range from 0-based coordinates
  -chr_stop        in gene docsum GenomicInfoType object

Sequence Flags

  -complexity    0 = default, 1 = bioseq, 3 = nuc-prot set
  -extend        Extend sequence retrieval in both directions
  -extrafeat     Bit flag specifying extra features
  -showgaps      Propagate component gaps

Subset Retrieval

  -start         First record to fetch
  -stop          Last record to fetch

Miscellaneous

  -raw           Skip database-specific XML modifications
  -express       Direct sequence retrieval in groups of 5 
  -immediate     Express mode on a single record at a time 

Format Examples

  -db            -format            -mode    Report Type
  ___            _______            _____    ___________

  (all)
                 docsum                      DocumentSummarySet XML
                 docsum             json     DocumentSummarySet JSON
                 full                        Same as native except for mesh
                 uid                         Unique Identifier List
                 url                         Entrez URL
                 xml                         Same as -format full -mode xml

  bioproject
                 native                      BioProject Report
                 native             xml      RecordSet XML

  biosample
                 native                      BioSample Report
                 native             xml      BioSampleSet XML

  clinvar
                 variation                   Older Format
                 variationid                 Transition Format
                 vcv                         VCV Report
                 clinvarset                  RCV Report

  gds
                 native             xml      RecordSet XML
                 summary                     Summary

  gene
                 full_report                 Detailed Report
                 gene_table                  Gene Table
                 native                      Gene Report
                 native             asn.1    Entrezgene ASN.1
                 native             xml      Entrezgene-Set XML
                 tabular                     Tabular Report

  homologene
                 alignmentscores             Alignment Scores
                 fasta                       FASTA
                 homologene                  Homologene Report
                 native                      Homologene List
                 native             asn.1    HG-Entry ASN.1
                 native             xml      Entrez-Homologene-Set XML

  mesh
                 full                        Full Record
                 native                      MeSH Report
                 native             xml      RecordSet XML

  nlmcatalog
                 native                      Full Record
                 native             xml      NLMCatalogRecordSet XML

  pmc
                 bioc                        PubTator Central BioC XML
                 medline                     MEDLINE
                 native             xml      pmc-articleset XML

  pubmed
                 abstract                    Abstract
                 apa                         PMID plus APA citation
                 bioc                        PubTator Central BioC XML
                 medline                     MEDLINE
                 native             asn.1    Pubmed-entry ASN.1
                 native             xml      PubmedArticleSet XML

  (sequences)
                 acc                         Accession Number
                 est                         EST Report
                 fasta                       FASTA
                 fasta              xml      TinySeq XML
                 fasta_cds_aa                FASTA of CDS Products
                 fasta_cds_na                FASTA of Coding Regions
                 ft                          Feature Table
                 gb                          GenBank Flatfile
                 gb                 xml      GBSet XML
                 gbc                xml      INSDSet XML
                 gene_fasta                  FASTA of Gene
                 gp                          GenPept Flatfile
                 gp                 xml      GBSet XML
                 gpc                xml      INSDSet XML
                 gss                         GSS Report
                 ipg                         Identical Protein Report
                 ipg                xml      IPGReportSet XML
                 native             text     Seq-entry ASN.1
                 native             xml      Bioseq-set XML
                 seqid                       Seq-id ASN.1

  snp
                 json                        Reference SNP Report

  sra
                 native             xml      EXPERIMENT_PACKAGE_SET XML
                 runinfo            xml      SraRunInfo XML

  structure
                 mmdb                        Ncbi-mime-asn1 strucseq ASN.1
                 native                      MMDB Report
                 native             xml      RecordSet XML

  taxonomy
                 native                      Taxonomy List
                 native             xml      TaxaSet XML

Examples

  efetch -db pubmed -id 6271474,5685784,4882854,6243420 -format xml |
  xtract -pattern PubmedArticle -element MedlineCitation/PMID "#Author" \
    -block Author -position first -sep " " -element Initials,LastName \
    -block Article -element ArticleTitle

  efetch -db nuccore -id CM000177.6 -format gb -style conwithfeat -showgaps

  efetch -db nuccore -id 1121073309 -format gbc -style master

  efetch -db nuccore -id JABRPF010000000 -format gb

  efetch -db nuccore -id JABRPF010000001 -format gb

  efetch -db protein -id 3OQZ_a -format fasta

  esearch -db protein -query "conotoxin AND mat_peptide [FKEY]" |
  efetch -format fasta -start 1 -stop 5

  esearch -db protein -query "conotoxin AND mat_peptide [FKEY]" |
  efetch -format gpc |
  xtract -insd complete mat_peptide "%peptide" product mol_wt peptide |
  grep -i conotoxin | sort -t $'\t' -u -k 2,2n | head -n 8

  esearch -db gene -query "DDT [GENE] AND mouse [ORGN]" |
  efetch -format docsum |
  xtract -pattern GenomicInfoType -element ChrAccVer ChrStart ChrStop |
  xargs -n 3 sh -c 'efetch -db nuccore -format gb \
    -id "$0" -chr_start "$1" -chr_stop "$2"'

  efetch -db sra -format docsum -id SRA030738,SRA030736 |
  xtract -pattern DocumentSummary -element Run@acc
