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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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