The Protein Sequence Alignment View provides graphical summaries of the aligned regions when a sequence search is performed. Aligned regions are represented using color code blocks that display the sequence identity through a gradient color code.
Alignment Conventions
- By default the fullQuery sequence is displayed excluding potential gaps.Query sequence is used as a reference to display the aligned regions. The alignment reference can be changed using the dropdown menu (SeeAlignment Reference)
- Aligned regions are displayed using blocks. When zoomed amino acid mismatches are displayed within red circles
- Blocks color correlates with the alignment sequence identity, from light blue (100%) to dark grey (25%) (SeeSequence Identity)
- White circles over start (or end) of blocks indicates that the aligned sequence continues in that direction but it is not part of the alignment
- White circles in the middle of blocks indicates a deletion in the aligned sequence
- Dashed line between blocks indicates that the aligned sequence is connected
Responsive and Interactive Properties
- Zoom using the mouse scroll (wheel) or the mousepad/touchpad to show the sequence amino acids an mismatches
- To zoom using the mousepad/touchpad hover over the Protein Feature View, and move/drag 2 fingers in an up and down motion
- Once zoomed, left click and drag to move the panel left or right (using either a mouse or touchpad)
Sequence Identity
Block color indicates the full alignment sequence identity using a gradient color fromBlue toDark Grey
representing alignment identity from 100% to 25%.
Alignment Reference
TheAlignment Reference drop down menu selects the reference that is used to display the aligned regions. By default theQuery option is selected to use theQuery sequence as reference. This means that the fullQuery sequence is displayed excluding any potential gap that could be found in the different alignments. TheQuery sequence is displayed in the first track of the Protein Sequence Alignment View. The bottom track displays the aligned regions of theEntity sequence includingEntity sequence gaps (orQuery sequence insertions) as dashed lines orEntity sequence deletions as white circles in the middle of blocks.
TheAlignment Reference can be changed toSubject. In this caseEntity sequences will be used as references. The first track of the Protein Sequence Alignment View will display the particularEntity sequence excluding any potential gap resulting from the alignment. TheQuery sequence is displayed in the second track includingQuery sequence gaps (orEntity sequence insertions) as dashed lines orQuery sequence deletions as white circles in the middle of blocks.
The thirdAlignment Reference option isPairwise. WhenPairwise is selected the Protein Sequence Alignment View will focus on the whole aligned section betweenQuery andEntity sequences displaying all details of the alignment including gaps in both sequences.
