Next: Appendix
Up: XPARALParametric Sequence Aligment
Previous: Program Controls
Generating an alignment of two sequences is both simple and fun. The following is a list of basic steps used to
generate the alignment shown on the XPARAL web page.
- Load the file containing two previously aligned strings. Select Load Aligned Strings from
the File menu. The filename is bartongo and the names of string 1 and 2 are
fabvl and fabvh, respectively.
If you don't have this file or wish to try out different sequences you can
type in your own in the sequence dialog boxes under the main menu bar.
- Now select a weight matrix. From the Scoring System
menu select PAM250 +8.For this decomposition we will use the PAM250 matrix that has been
normalized by adding 8 to each entry.
- Choose the parameters, from the Opt Function menu select
(#matches)-(#mismatches)-X*(#indels)-Y*(#gaps).
- For this alignment we will use the default ranges for the X and Y axies and the default values
for the constants c1 and c2. However, they can be changed with the ranges or constants
menu options.
- Choose the gap model from the Gap Type menu. For this alignment we will use the affine model so
select g(x)=x.
- Now it is possible to decompose the entire parameter space by selecting Find All Polygons from
the Get Polygons menu. It should finish in just a few seconds.
- Once the parameter space has been decomposed you can click on any polygon to view the optimal
alignments generated for the range of parameters it encompasses. You can even scroll through the co-optimals
using the Prev and Next buttons.
- Now try saving the alignments generated in one polygon. From the File menu choose
New Log File. Enter the name of the file you wish your alignments to be saved in, e.g.
alignments.log, and click the OK button. You can click on the polygon containing the
alignments you wish to save and select Save Dark Polygon from the File menu. A dialog
box should appear containing the name of the log file, all you need to do is click OK.
- Now see what the decomposition looks like with convex gaps. Choose g(x)=log(x) from the
Gap Type menu. You can now select Find All Polygons from the Get Polygons menu
to see the new decomposition. Note: this will take a bit longer.
Next: Appendix
Up: XPARALParametric Sequence Aligment
Previous: Program Controls
Kristian Stevens
1998-10-13