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Batch Entrez

Batch Entrez

Given a file of Entrez accession numbers or other identifiers, Batch Entrez downloads the corresponding records.

Instructions

  1. Start with a local file containing a list of accession numbers or identifiers
  2. Select the database corresponding to the type of accession numbers or identifiers in your input file
  3. Use the Browse or Choose File... button to select the input file
  4. Press the Retrieve button to see a list of document summaries
  5. Select a format in which to display the data for viewing, and/or saving
  6. Select 'Send to file' to save the file.

Tips

  • To download entire genome records, check the NCBI FTP site, instead of using Batch Entrez.
  • Some lists of record identifiers can be tens of thousands of lines long, so Batch Entrez may not retrieve all records from one list. Split the list of identifiers into smaller files using a file splitting software or a file split command at the command prompt in UNIX or LINUX systems.
  • When loading large numbers of genome records, put several thousand record identifiers per file, one per line, left-adjusted.
  • Please note that Batch Entrez will check for duplicate identifiers when reporting results from a list that you have imported.
  • When retrieving a list of Nucleotide accessions, you must select the specific component database from which the accessions or GIs were saved. For Nucleotide, choose either the CoreNucleotide, the EST or the GSS selection from the database menu. If you have a mixed list of nucleotide accessions or UIDs, you will need to run the Batch Entrez search three times. Select the database from the pull-down menu, CoreNucleotide, EST, and GSS separately.
  • In all cases, be certain to select the database that corresponds to the identifiers you are uploading. For example, if you have saved a list of protein accession numbers, be sure to select the Protein database.