Program Controls

The main XPARAL window (boxed) is used to display the parametric decomposition. It should be maximized to best fit with the vertical text.

XPARAL finds the parametric decomposition of two strings which are displayed just above the main window. The program is initiated with two default strings, both aligned to the left margin without inserted spaces. These input strings can be changed by the user as described below. As XPARAL runs, it finds and displays each successive polygon and changes the displayed alignment of the two stings. The alignment then shown is an optimal alignment for the most recently found polygon, which is displayed darker than the other polygons. In the displayed optimal alignment, matches are outlined in color and with a carrot below each match. Once the full decomposition is finished, the user can explore it by clicking the mouse in any polygon. The optimal alignment for that polygon is then displayed.

Below the two strings the word VAR is written. Before the parametric alignment is computed, what follows VAR is a description of the parameter choice currently in effect. Whenever an alignment is computed for a polygon, that description is changed to show the number of matches, mismatches and indels in the current alignment, and the number of gaps if an objective function using gaps has been chosen by the user.

It is possible to use different alignment types, such as global, local, end gaps free, or substring. An OPT window displays the currently selected alignment model.

The chosen boundaries for x and y, and the chosen constant(s) c1 and c2 (when gaps have been chosen) are also displayed. If weight tables are used for the alignment of two sequences the name of the weighting scheme is also displayed.

The main XPARAL menu contains the following selections:

FILE

This is the main file menu.

• Load Aligned Strings This menu option pulls up a dialog box in which you can input a stored alignment. You must know the names of the two aligned sequences in addition to the name of the file.
• Load String Loads a text file as a single string, it can be loaded as either string 1 or 2. The file is loaded in as raw text.
• Save String Saves a single string as a text file, either string 1 or 2 can be saved. A dialog box will appear prompting for the name of the file.
• Reverse String Reverses either of the strings already inputted so that it appears backwards.
• Save All Polygons Saves all of the polygons in the decomposition. You must open a logfile before this operation can be performed.
• Save Min Distance Polygon Saves the polygon of minimum distace from an input alignment. You must open a logfile before this operation can be performed.
• Save Dark Polygon Saves a single selected polygon (appears dark). You must open a logfile before this operation can be performed.
• Save Polygon Alignments Saves the alignments for a polygon but not the geometry. You must open a logfile before this operation can be performed.
• New Log File A dialog box will appear prompting for the name of a log file in which alignment information can be saved. This must be done before any polygons can be saved.
• Quit Exits the program.

ALIGNMENT

This menu allows the user to select the alignment model. The four primary schemes are as follows:

• Global (Needleman-Wunsch style) Global alignment finds the best alignment between the entirety of the two input sequences.
• End Gaps Free This alignment scheme causes end gaps to have no penalty. This will favor optimal alignments between the beginning of sequence 1 and a end of sequence 2 and vise versa. Free spaces are indicated by ~, while spaces that are scored are indicated by -. When local alignment is chosen, the optimal substrings are enclosed in brackets [ ].
• Local (Smith-Waterman style) This alignment sceme will find the maximum optimal alignment amongst all combinations of substrings from sequence 1 and 2. Free spaces are indicated by ~, while spaces that are scored are indicated by -. When local alignment is chosen, the optimal substrings are enclosed in brackets [ ].
• 1st as a Substring of 2nd This will find the optimal alignment amongst all of the possible substrings of sequence 1 with the entirety of Sequence 2. Free spaces are indicated by ~, while spaces that are scored are indicated by -. When local alignment is chosen, the optimal substrings are enclosed in brackets [ ].

OPT FUNCTION

This menu allows the user to select the alignment optimization function. The choices for parameterization include all ways of picking two terms to parameterize from the four terms: match, mismatch, indel, gap. For convenience (and efficiency of the program), the cases when gaps (but not indels) are given a zero penalty are listed separately. The following equations are supported where a parameterized variable appears as the name of an axis, and a constant appears either as c1 or c2. These constants are by default set to 1.0, but can be changed by the user.

• (#matches)-X*(#mismatches)-Y*(#indels)
• X*(#matches)-(#mismatches)-Y*(#indels)
• X*(#matches)-Y*(#mismatches)-(#indels)
• (#matches)-(#mismatches)-X*(#indels)-Y*(#gaps)
• (#matches)-X*(#mismatches)-(#indels)-Y*(#gaps)
• (#matches)-X*(#mismatches)-Y*(#indels)-(#gaps)
• X*(#matches)-(#mismatches)-(#indels)-Y*(#gaps)
• X*(#matches)-(#mismatches)-Y*(#indels)-(#gaps)
• X*(#matches)-Y*(#mismatches)-(#indels)-(#gaps)

CONSTANTS

This menu allows the user to set the values for constants. Normally it should be selected after the optimization function has been chosen.

RANGES

This menu allows the user to set the ranges for the parameters.

GAP TYPE

This menu allows the user to select the gap model from the three that are currently available. XPARAL will use different algorithms and datastructured based on the chosen gap type. Convex gap models will run slower than affine and currently they can only be used with global alignments.

• g(x)=x Affine gap model where the cost to extend the gap is always 1.
• g(x)=log(x)+1.0 Convex gap model, log version, where the total gap cost is gap init + g(x). Note the added 1.0, this insures that a gap of size 2 is always more expensive than two gaps of size 1.
• g(x)=log(x + 1.0) Convex gap model, log version, where the total gap cost is gap init + g(x). Note the added 1.0, again this insures that a gap of size 2 is always more expensive than two gaps of size 1.
• g(x)= root(x) Convex gap model, root version, where the total gap cost is gap init + g(x).
• g(x)= root(x)+1.0 Convex gap model, root version, where the total gap cost is gap init + g(x). Note the added 1.0.
• g(x)= root(x+1.0) Convex gap model, root version, where the total gap cost is gap init + g(x). Note the added 1.0.

SCORING SYSTEM

Choose the method of scoring matches and mismatches. The defaule is not to use a scoring matrix. However many scoring matricies are included with the program, you also have the option of loading your own.

• No Scoring Matrix If you are using a scoring matrix you can turn it off with this.
• PAM 250
• PAM250 + 8
• McClure
• Gonnet
• Gribskow
• Taylor
• Other Scoring Matrix Load your own scoring matric file.

GET POLYGONS

Generates the optimal alignments.

• Find All Polygons Decomposes the entire parameter space into convex polygons.
• Find Closest to Input Alignment Finds the closest alignment polygon to an Input Alignment.
• Find Polygon(s) for Point Finds the polygon(s) that contain a single point chosen by the user.