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

Refining a subsequence search
You can refine any of your searches by using one of the radio buttons. The default setting
is Exact Matches.
Exact matching
If you click Exact Matches the search is based on exact character matches and
disregards matches that occur due to ambiguities. For example, AGGTW would only
match AGGTW.
Matching ambiguous bases
If you click Specified Bases the search finds only matches that are identical or more
specific than the sequence you entered in the Find What: field. For example, the string
AGGTW would match AGGTT or AGGTA, since W is the ambiguity code for T or A.
Any ambiguous match
If you click Any Ambiguous Match the search will find any degenerate DNA that may
match the sequence you have entered, including matches consisting of all unknown bases.
For example, AGGTW would match NNGTN or even NNNNN.
Finding bases by number
To select a range of bases quickly, go to the Select menu and choose Bases by Number.
A dialog box lets you enter the range of bases you want to highlight.
Extend Selection
You can extend the current selection to the beginning or end of your sequence by going
to the Select menu and choosing Extend Selection. Then choose the suboption to Left
End or To Right End.
Note: In a contig chromatogram the Extend Selection command can extend your
selection across the entire sequence in one click.
Other search options
You can also search for ambiguous bases by going to the Select menu and using the Next
Ambiguous Base command. You can search for edited bases using the Next Edited
Base option. (These are described in more detail in Chapter 8 “The Sequence Editor”.)
You can also search for potential open reading frames using the Next Met to Stop (> 0b)
option. (This is described in more detail in Chapter 21 “Customizing Sequencher and
User Preferences.”)
Project Window selection
Finding an item by name
To locate a specific sequence or contig, select the Project Window. Type the name of the
item you are trying to find, for example, ‘Sequence C.’ As you type, Sequencher starts
looking in the Project Window for an icon with the name you are typing and highlights a
match. If it finds more than one, it highlights the first one.
SEQUENCHER 4.8 User Manual for Windows © 1991 - 2007 Gene Codes Corporation, Inc. All rights reserved.
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