Downloading sequences with Entrez

GeneStudio's Entrez interface provides an easy way to search GenBank using the Entrez utility and retrieve the sequences from within SeqVerter, the Alignment editor or the Contig editor.  Hits can be downloaded and optionally automatically opened.

To perform an Entrez search:

  • Select the NCBI Entrez menu item from the Internet menu.
  • Enter up to four search terms.
  • Select the database to search, protein or nucleotide.
  • Select the maximum number of sequence hits to return.
  • Select any date restrictions required.
  • Press the Submit button.

When the search is complete, the Entrez results dialog box will be displayed.


Entrez Search dialog reference table:

Search

  • Search terms
    Enter a search term such as the organism name, locus or author.
  • Search fields
    Select an Entrez database field to restrict search.
  • Radio buttons
    Combine this search term with other search terms using the logical AND, OR, and NOT operators.

Select database

  • Proteins
    Search the Entrez protein database.
  • Nucleotides
    Search the Entrez nucleotide database.

Limit entry download

  • Max entries to download
    Restrict the number of entries to display in the Entrez results dialog box.
  • Oldest entries
    Restrict the search by date.

Commands

  • Submit
    Submit the query to the NCBI server.
  • Stop
    Abort the current search.
  • Reset
    Clear the search form.
  • Exit
    Close this dialog box.

Entrez results viewer reference table.

The Entrez results viewer is displayed automatically when a search is complete.  This dialog box lists the sequences with check boxes beside the sequence name.  Select sequences for download using the check boxes.  Selected sequences can be saved to disk or they can be saved and automatically opened in SeqVerter or the Alignment editor.

Hit sequence list

  • List box
    List of Entrez hit results.  The sequence name and definition line are displayed.  Check boxes beside the sequence names are used to select sequences for downloading.  Double-click on the sequence name to view the hit sequence's NCBI GenBank entry in your web browser.
  • Select all
    Select all sequence in the results list for downloading.
  • Deselect all
    Deselect all sequence in the results list for downloading.
  • View in browser
    View the highlighted sequence's NCBI GenBank entry in your web browser.

Options

  • Save only
    Download the selected sequences without opening them.
  • Save and open in SeqVerter
    Download the selected files, then open them in SeqVerter.
  • Save and open in the Alignment editor
    Download the selected files, then open them in the Alignment Editor.

Download folder

  • Edit box
    Enter the folder path for downloaded files.
  • Browse button
    Select the download folder using the Browser for folder dialog box.
  • Import folder
    Use the default import folder.
  • Export folder
    Use the default export folder.
  • Last folder used
    Use the last folder visited.

File names

  • Locus
    Use the hit sequence locus name for the downloaded file name.
  • Accession number
    Use the hit sequence accession number for the downloaded file name.

Action

  • Exit
    Close this dialog box.
  • Import and exit
    Close this dialog box and the Entrez search results dialog box after downloading.
  • Import and return to Entrez results
    Close this dialog box and return to the Entrez search results dialog box after downloading.
  • Cancel download
    Abort the current download.