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

Figure 9-2 The Clean Data algorithm with Maximum Loop Out Size shown
Assembling with Large Gap
The Large Gap algorithm is specifically for data that has or might have large insertions or
gaps. This might include data from evolutionary studies, different organisms or comparing
cDNA to genomic DNA. When you select the Large Gap algorithm, there are two sliders
for changing minimum match values. To set the proportion of bases that have to match
use the Minimum Match Percentage slider. To set the minimum number of bases that
must overlap use the Minimum Overlap slider.
Note: Assemble to Reference cannot be used with the Large Gap algorithm.
Assemble By Name
You can enable Assemble By Name by clicking in the checkbox called Enabled. Click
the Names Settings... button. Choose your delimiter from the Name Delimiters drop
down menu. Then type names for the Assembly Handles into the fields in the Assembly
Handles pane.
To activate an Assembly Handle, click the adjacent radio button. When you are done,
click the OK button.
You will notice that the drop down menu in the Assemble By Name pane under the
Assembly Parameters window now contains the names of your handles.
Next to each handle is a number enclosed in square brackets. This indicates the probable
number of contigs you can generate using that handle.
If you want to use a more complex delimiter, you must select Advanced Expression…
from the Name Delimiters drop down menu. Clicking the Define… button will take you
to the Advanced Expression for Name Parsing window. In this window, you write and
preview the regular expression you want to use. You can find more information on regular
expressions by going to Appendix 24 “Advanced Expressions,” or for more detail, consult
the tutorial in the Sequencher Tutorials folder.
You can find more information on Assemble by Name in Chapter 10 “Assemble
by Name”. For information on regular expressions see Appendix 24 “Advanced
Expressions,” or for more detail, consult the tutorial in the Sequencher Tutorials folder.
SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved.
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