Pair Alignment Display Help

Overview: The core of the display is a standard text alignment of all or some of the residues in the sequences aligned. Amino acids are shown with the standard one-letter code and indels (gaps) are denoted with dashes in the shorter sequence ("-"). Alignment positions are shown at the top row. Residues are shaded to indicate the quality of their local match score, with darkest blue being the best, white being zero, and pink being all negative scores. The specific score for any single matched residue pair or gap can be gotten by allowing the mouse to hover over one of the residues. Because there are only two sequences involved, scores are always the same for both residues. For example, for a residue opposite a gap you might expect that the residue would get a better score but this is wrong because it cannot be known whether the gap arose by deletion of the residue in one sequence or insertion of the residue in the other. You can learn a lot about the scoring and alignment methods by checking the numerical scores in many places. For example, where there is a gap of more than one residue the first gap position will have a score that reflects the gap open penalty and subsequent positions will have a score reflecting the gap extend penalty (typically much lower). Often a more realistic sense of local alignment quality can be gotten by viewing a score that averages across several local residues (see score window).

Score Window: This setting controls how many aligned residues are averaged to produce the score shading and number. The default display is set to one, meaning that the score shading for each residue reflects the score quality only at that single position. Larger score windows cause each position to be assigned a score based on the average of it and residues around it. Try increasing the score window to see how the quality blurs out as the window increases.

Selecting Residues for Realignment: You can realign any part (or all) of the current alignment by highlighting the residues and using the menu "Align : Align Selected Columns". You can use this simply to manage easily viewed regions of an alignment, but more importantly, you can change the alignment parameters for realignments. Use the menu "Align: Pair Align Parameters" to bring up the standard Pair Align Settings dialog, which can be used to change these parameters. The default will be the same as for your original alignment except that Dot Matrix Display will be turned off since this is less likely to be useful (you can always turn it back on). Changes you make here will not affect the settings from the main window.

Interpreting Alignment Quality: The color coding and the numerical scores are given in "half-bit" scores because this is the standard for score matrices. A "bit" value is simple to interpret: one bit indicates a 2-fold difference in the probability that this alignment pair differs from that expected by chance alone. For example, a bit value of 0 indicates a match that is found just as often in real alignments vs. chance alignments, a bit value of +3 bits (which is +6 in the half-bit score) indicates a match that is 8-fold more common in real alignments than in chance alignments, and a bit value of -2 (a score of -4) indicates a match that is 4-fold less common.

Notes on Alignment Quality: The alignment shown is guaranteed to be a best-scoring alignment for these two sequences given the assumptions implicit in the alignment model (see Score Matrix Help for specifics). However, there is NO GUARANTEE that there aren't other alignments that are very close to this one in score, or even equal in score. Unless the sequence has unusual features like repeats with high similarity, these other alignments will be relatively modest variants on the "best" alignment, but they can be highly significant in local regions of the alignment. [I may add alternative opitimal or near suboptimal alignment paths in the future]


File Menu:

Save as Multiple Alignment: Save this multiple alignment in Bonsai serialized format.

Save as Interchange Multiple Alignment: Save this multiple alignment in the Bonsai text interchange format.

Save Sequences: Save the sequences in this pair alignment as a Bonsai format sequence file. This is a convenient way of saving trimmed sequences for core alignments.

Save As GIF: Save this pair alignment as a GIF file. [Incompletely implemented]

Print: Print this pair alignment. [Incompletely implemented]


View Menu:

Single/Multiple Block Display: A pair alignment initially displays on a single line for each sequence. To show the alignment in multiple blocks, use this menu item. In multiple block mode, several features will be disabled because they are a pain to program [I may fix this]. Make changes in single block display first, then switch to multiple block.

Show/Hide Alignment Comments: You can display and edit comments on this alignment in a pane that will appear at the bottom of this window. If you use and then close the comments pane or if you have added comments and save the alignment, changes will automatically be saved.

Score/Hydrophobic Color: The Bonsai default is to show the score quality colors. Use this menu item change shading to degree of hydrophobicity.

Increase/Decrease Score Color: Intended to tune the output visibility for different monitors and projectors. The background color intensity changes. This doesn't change anything about the alignment itself or the scores, but it will be reflected in the colors when saved or printed.

Show/Hide Negative Color: The Bonsai default is to show negative score colors in light red. This is a useful warning for poor alignment regions, but you can turn it off using this menu item.

Show/Hide Gap Color: The Bonsai default is to hide colors for gap residues as they can be distracting (for example, a column with mostly gaps shows these as scoring highly!). Use this menu item to show the computed colors for gaps.

Show/Hide All Color: The Bonsai default is to show the score quality colors. Use this menu item to remove or reinstate the colors.

Boxshade: To view the alignment in the more familiar Boxshade format. Useful mostly for black and white figures. [note - incompletely implemented]

Residue Number/Alignment Score Tooltips: The default is to show the residue number when the cursor hovers over an alignment residue. Use this menu item to toggle between this mode and one in which the local alignment score for the residue is shown.


Align Menu:

Align Selected Columns: Realign all the sequences using only the selected residues. You must be in Column Select mode for this to be active.

Alignment Bootstrap Test: Use repeated sequence shuffling and realignment to test the significance of this pair sequence alignment.

Pair Alignment Settings: Change the pair alignment settings that will be used in further alignments starting from this window.


Help Menu:

Pair Alignment Help: This help.


James H. Thomas, Department of Genome Sciences, University of Washington
8/8/2002