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.

The Pairwise view displays the query sequence aligned pairwise to a BLAST search match. This view is nearly identical to the same view in the Lasergene application MegAlign Pro.

To open a pairwise alignment for any completed BLAST results, do any of the following:

  • Go to the Jobs panel (View > Jobs) and click on the Done link for a completed BLAST search job. A new window will open with the Table view on top and the Pairwise view on the bottom.
  • If the view has been closed, return to it by clicking on the Pairwise tab ().
  • If the Pairwise view is open but you want to view results for a different BLAST search job, use the menu in the top left corner of the view to select the job.

The summary area near the top of the view describes the alignment engine and settings that were used to create the pairwise alignment. Protein alignments always use the BLOSUM62 matrix, while nucleotide alignments use NUC44. This section features a one-row table whose columns are described below.

Value Description
(Query name) The query ID with the range of nucleotides or amino acids that were included in the query shown below the name.
(Target name) The accession number of the matching database entry with the range of nucleotides or amino acids included in the match shown below the accession number.
% Identity Number of matching residues divided by the sum of all residues and gap characters. The quotient is multiplied by 100 to give the similarity as a percent.
% Gaps The gap length divided by the consensus length. The quotient is multiplied by 100 to give the similarity as a percent.
Identical Number of residues that are identical in both sequences.
Gap Count Number of gaps (of any length) in either sequence of an alignment.
Gap Length Number of gap characters in an alignment.
Score The cumulative score for an alignment derived by adding the matrix-derived match scores and subtracting gap penalties.
Length Number of residues in the consensus, including gaps that match in both sequences.

Below the summary area is the colorful sequences area. For each sequence, the amino acid codes are displayed on the right, and their labels on the left. The order is always “query sequence” first, and “target sequence” second. The blue consensus ruler numbers and ticks any gaps found in the consensus.

Click the plus sign at the left of a row to reveal two tracks: Gap Fraction and Ruler. These default tracks cannot be edited, and additional tracks cannot be displayed.

  • Gap Fraction – If data is available, displays a graph track with a scale of 0-1 that shows the proportion of gapped positions in a sliding window centered on each position.

  • Ruler – The black gap-aware sequence ruler uses pre-alignment numbering for the sequences.

Tasks that pertain to the Pairwise view:

Task How To…
To create a new pairwise alignment using a different target sequence Make a selection from the drop-down menu at the top of the view. The target sequence should be the same length or longer than the query. (Note that the Query drop-down menu has an unchangeable default sequence).
To zoom in or out The Pairwise view features independent vertical and horizontal zoom in/out sliders. Grab a green slider with your mouse and drag left/right or up/down to zoom in or out in the view.

To display data tracks See the topic Tracks panel.
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 matches 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 export an image of the alignment Use the Export alignment as image tool () in the upper right corner of the view. Images can be saved in PDF (.pdf), PowerPoint (.pptx), PNG (.png) or JPEG (.jpg) formats.
To change the layout of the view or what is displayed in it See Customize the look and layout.

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