Beckman Coulter CEQ 8000, User Manual

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Sequence Analysis Procedures
162 CEQ™ 8000 Genetic Analysis System
Check
Find matching substrings
to optimize the alignment. When the
alignments are optimized, the system will find matching substrings first, then run the
alignment algorithm on the bases remaining outside of the substrings, reducing the
execution time and storage space.
Check the
Find Local alignment
to use only the substrings with the highest score,
ignoring the rest, as opposed to using every character from both strings to compute the
similarity score.
Check
Left Edge Free
and/or
Right Edge Free
to specify that overhanging bases
on the template or sequence will not be counted in the alignment score.
Enter the number of bases needed to constitute a substring in the
Minimum
substring length
text box to specify a minimum length for detected substrings. The
range is 5 to 2000. A value of 30 is the default value.
If a value is outside of an expected range, a message box will be dis-
played requesting that a valid value be entered.
Quality-based Trimming Tab
Use Quality-based trimming to trim poor quality data from the ends of the sequence.
The resulting Base Sequence and Trace Views display the base letters of the poor
quality data as strikethrough.
Figure 98: Quality-based Trimming tab