Sequencher 4.8 User Manual--PC - Bioinformatics and Biological ...

Interactive assembly
The Assemble Interactively algorithm can be used whenever you want complete
control over the assembly of a batch of sequences. The Assemble Interactively
window provides you with detailed information regarding overlap, mismatch and
gapping for any given sequence and a set of candidate sequences. The candidate
assemblies are driven by your user-defined assembly parameter settings.
Performing an interactive assembly
Bring the Project Window to the front and select the items you want to assemble.
Click on the Assemble Interactively button at the top of the Project Window or go to
the Contig menu and choose Assemble Contigs and then Interactively… from the
submenu.
Sequencher displays the Assemble Interactively dialog box shown in Figure 9-4. The
sequences and contigs you selected are displayed in the Candidates list. The panel on the
right, showing a face in the upper left corner, is called the “agent.” It displays information
about the comparisons you have requested. In the center is the Matches panel which
displays the possible matches. For each match in the panel Sequencher lists the % Match,
the approximate number of Overlap bases, the number of Mismatch bases, the number
of Gaps and the New Contig Length.
The top line shows the Candidate sequence and the line below this shows the Match
sequence. Below these two lines is the consensus sequence. There is a small button to the
right of the consensus labeled with a black circle. If you click repeatedly on this button
you can display the first, second, third reading frame or all three reading frames at once.
The label on the button changes to reflect which of these choices is active.
Figure 9-4 Assemble Interactively dialog box
To have Sequencher compare any single sequence or contig with the other items in the
Candidates list, click on the name of that sequence or the contig in the Candidates list.
When the comparison is complete, the possible matches appear in the Matches list to the
right of the Candidates list, as shown in Figure 9-5.
SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved.
69