Sequencher 4.8 User Manual--PC - Bioinformatics and Biological ...
Sequencher 4.8 User Manual--PC - Bioinformatics and Biological ...
Sequencher 4.8 User Manual--PC - Bioinformatics and Biological ...
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Saving a duplicate of a current project ...................................................................................................... 31<br />
Reverting to the saved version of the project. ........................................................................................... 31<br />
Closing the Project Window...................................................................................................................... 32<br />
Exporting data ........................................................................................................................................... 32<br />
Exiting the program................................................................................................................................... 32<br />
6. PREPARING YOUR DATA FOR ASSEMBLY ..............................................33<br />
Removing undesirable data ............................................................................................... 33<br />
Trimming poor quality data .............................................................................................. 33<br />
Selecting <strong>and</strong> trimming fragment data ...................................................................................................... 33<br />
Performing a trim with default settings ..................................................................................................... 34<br />
Automatically selecting sequences for ends trimming .............................................................................. 34<br />
How to set the Ends Trimming criteria ..................................................................................................... 34<br />
Using Confidence to Trim Ends ................................................................................................................ 35<br />
Reviewing the Trim ................................................................................................................................... 35<br />
Sorting items ............................................................................................................................................. 36<br />
Executing the trim ..................................................................................................................................... 36<br />
Trimming vector contamination ........................................................................................ 37<br />
Selecting sequences for Vector Trimming ................................................................................................. 37<br />
Specifying a vector using VecBase ........................................................................................................... 37<br />
Specifying the insertion site manually ...................................................................................................... 39<br />
Saving <strong>and</strong> loading vector sites ................................................................................................................. 39<br />
Setting Vector Trimming Criteria .............................................................................................................. 40<br />
How <strong>Sequencher</strong> screens sequences ......................................................................................................... 41<br />
Executing the trim comm<strong>and</strong> .................................................................................................................... 41<br />
7. THE REFERENCE SEQUENCE .................................................................. 43<br />
What is a Reference Sequence ........................................................................................ 43<br />
Why use a Reference Sequence ............................................................................................................... 43<br />
Reference Sequence properties ......................................................................................... 43<br />
Basic Reference Sequence properties ....................................................................................................... 44<br />
Working with a Reference Sequence ................................................................................ 45<br />
How to mark a sequence as a Reference ................................................................................................... 45<br />
Assemble to Reference .............................................................................................................................. 45<br />
To Reference by Name .............................................................................................................................. 45<br />
Trim to Reference ...................................................................................................................................... 46<br />
Contig Editing with a Reference Sequence ............................................................................................... 46<br />
Fill Coverage Gaps with Reference .......................................................................................................... 47<br />
Reference Sequence Translation ............................................................................................................... 47<br />
8. THE SEQUENCE EDITOR ........................................................................... 49<br />
Opening an existing sequence for editing ................................................................................................. 49<br />
Locked Editors .......................................................................................................................................... 49<br />
Basic sequence editing .............................................................................................................................. 50<br />
Setting the base numbering ....................................................................................................................... 51<br />
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