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

7. The Reference Sequence
In this chapter we explain Reference Sequences – sequences or fragments used as
baseline or benchmarks for subsequent comparison. We will describe the special features
of Reference Sequences. We will then discuss how to designate a sequence as a Reference
for your project, how to assemble sequences to the Reference and how to edit contigs
containing a Reference Sequence.
What is a Reference Sequence
A Reference Sequence is any sequence that you have selected to act as a model for your
subsequent comparisons. You may have obtained this sequence from one of the public
DNA databases or you may have characterized it yourself. Once you have marked your
sequence as a Reference, Sequencher attaches certain properties to it.
Why use a Reference Sequence
There are many situations where you might want to designate one fragment in a project
as a Reference Sequence. In forensics, human identification depends on comparing
differences with a standard reference sequence. In medical genetics, a lab might want
to compare the same gene from family members to the specific variant that is known to
be part of a disease process. In a population study, a lab might compare the same gene
from thousands or tens of thousands of individuals to a wild type sequence. In all of these
circumstances, using Sequencher’s Assemble to Reference command with a Reference
Sequence allows you to pinpoint mutations and variants rapidly.
Reference Sequence properties
Before you start work with the Reference Sequence, you should be aware of a number of
important properties.
SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved.
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