After the Jobs panel shows the Status of a BLAST search or Entrez search is Done, pressing the “Done” hyperlink opens the search results simultaneously in the Text, Table, and Pairwise views. All three views are contained in a large pop up window that is separate from the main Protean 3D window.

If no significant matches were identified, the Table view will be empty. An example of a populated Table view is shown below:

Columns in the view’s table are described below:

Column Description
Accession The NCBI “Accession” number for the match. Press the link to open the corresponding page on the NCBI website.
Description The NCBI “Definition” field text.
Score The similarity score for the match. (See the NCBI definition for raw score). In general, a higher score denotes a better match.
E-Value The chance that the match is expected to occur by chance. (See the NCBI definition for E value). In general, a lower score denotes a better match.
%Coverage The percentage of the query sequence that aligns to a match in the BLAST database.

Example: Query has 596 bases, of which 565 align to a match in the NCBI database. %Coverage = 565/596 = 95%.
%Identity The percentage of bases that match when the query and result sequence are aligned. (NCBI definition).

Example: Query has 565 bases that align to the match and 3 bases that don’t match. %Identity = 562/565 = 99.5%.
Map Graphic showing areas of agreement between the query and the match.


Tasks that pertain to the Table view:

Task How To…
To launch the NCBI page for matching database entry Click the hyperlink in the table’s Accession column.
To copy all information from a search result row Right-click on the row and choose Copy.
To save the sequence match in .gbk format Right-click on the row and choose Download sequences. In the ensuing Save As dialog, choose a location in which to save the sequence. By default, the sequence is named using its Accession number.
To display a different search job Select it from the drop-down menu in the upper left of the window ().
To display a pairwise alignment using a particular search result If both the Table and Pairwise views are open, click on the desired row in the Table view to see the corresponding pairwise alignment in the Pairwise view. As an alternative, open the Pairwise view manually and choose the desired target from the with drop-down menu.
To display search results for previous query (in a single job with multiple queries) Use the Previous query tool ().
To display search results for the next query (in a single job with multiple queries) Use the Next query tool ().
To filter results from a sequence search Use the Filter results tool (). Filtering for this situation is described here.
To filter results from a text search Use the Filter results tool (). Filtering for this situation is described here.
To add sequences or matches Use the Add sequences or subsequences tool (). Sequences are added back into the host application, not the job’s document.
To launch the Search Online dialog Use the Change search strategy tool (). See Search for Sequences Online for details.
To save the search job to disk Use the Save as tool ().
To export data from the view Use the Export data tool ( ), described in the topic Export data from the Text, Table or Pairwise views.
To show the active view in full-screen mode Use the View > Full Screen command or the the Full screen tool at the bottom right corner of the view.
To exit full screen mode Press the Esc key or use the Exit full screen tool ) at the bottom of the full-screen view.
To configure the number and location of visible views. Use the View > Change layout command or the Change layout tool (image varies) in the bottom right corner of the view. The following options are available:

  • One – To show only the current view.
  • Two Horizontal () – To show the current view on top and one additional view below it.
  • Two Vertical () – To show the current view on the left, and one additional view to the right.
  • Three Horizontal () – To show the current view on top and two additional views below it.
  • Three – Left () – To show the current view on the left and two additional views stacked one on top of the other on the right.
  • Three – Right () – To show the current view on the right and two additional views stacked one on top of the other on the left.
  • Three – Top () – To show the current view on the top and two additional views side-by-side on the bottom.
  • Three – Bottom () – To show the current view on the bottom and two additional views side-by-side on the top.

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