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

10. Assemble by Name
Many labs apply strict sample-naming conventions to their sequences, with the name
indicating something about the data. Assemble by Name harnesses the information from
your sequence names to automate the process of selecting and naming your contigs.
In this chapter, you will learn how to use Assemble by Name, a powerful tool that lets
you separately assemble and automatically name multiple contigs from a single selection
and assembly command. For example, in just a few clicks of the mouse, Assemble by
Name will create ninety-six appropriately named contigs from ninety-six forward and
reverse sequences.
The Assemble by Name Strategy
The names of your samples frequently contain information such as your primer, template,
clone name or sample source. Sequencher provides you with tools to separate the
descriptive parts of your sequence name and use these to manage the assembly. These
tools are the Assembly Handles and the Name Delimiters.
An Assembly Handle is any set of characters from your sequence name that provides
information about that sequence, such as the primer or clone name. A Name Delimiter
separates each Assembly Handle from the following one. Sequence names frequently
have several Assembly Handles and Name Delimiters.
In its simplest form, a Name Delimiter may be a character such as a dash or an
underscore.
SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved.
73