Beckman Coulter CEQ 8000, User Manual

Page: 177 / 382

Analyzing Sequence Data
User’s Guide 163
Ends To Be Trimmed
Click the radio button to select the end(s) to be trimmed. Select
Both Ends
to trim
outside the 5' and 3' coding region. Select
Left (5') End
to trim to the left of the 5' end
or select
Right (3') End
to trim to the right of the 3' end. If
None
is selected, no
quality-based trimming will be conducted.
Trimming Stringency
The slider control sets the quality values from low to high. There are five possible
selections ranging from Low to High that correspond to error rate of 0.07, 0.06, 0.05,
0.03, 0.01. The default value is Medium (5%).
Sequence-based Trimming Tab
The Sequence-based trimming function allows for contaminant (sequence-based)
trimming. This can be done in Batch Analysis mode or in Sequence Analysis mode.
The resulting Base Sequence and Trace Views display the base letters of the vector and
other subsequences as underlined. If multiple vector or subsequences matched, they
will appear as multiple underlined in the Trace View.
The most common sources of contamination are accessory DNAs that have been
deliberately attached to the DNA under investigation. These include:
• Vector Sequences such as plasmid, phage, BAC, PAC and cosmids
• Primer Sequences
• Restriction Enzyme Sites
Figure 99: Sequence-based Trimming tab