GELDISASSEMBLE

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Table of Contents
FUNCTION
DESCRIPTION
EXAMPLE
RELATED PROGRAMS
COMMAND-LINE SUMMARY
LOCAL DATA FILES
PARAMETER REFERENCE

FUNCTION

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GelDisassemble breaks up the contigs in a fragment assembly project into single fragments.

DESCRIPTION

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See the Fragment Assembly System (FAS) Introduction for an overview of working with the programs within the FAS to assemble sequences in a sequencing project.

GelDisassemble breaks all assembled contigs in the current fragment assembly project and rebuilds a database consisting of the unjoined, working fragments. All edits made to the fragments in GelAssemble are preserved in the unjoined fragments.

You can rebuild the database from the original gel readings, rather than the working fragments, using -ARChive. This recreates the project database exactly as if you had just entered all of the fragments. Any modifications you have made to the sequences in GelMerge and GelAssemble are lost.

EXAMPLE

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Here is a session with GelDisassemble used to disassemble the project "myproject." This project was created in the example sessions of GelStart, GelEnter, and GelMerge.


% geldisassemble

 Are you sure you want to disassemble your project (* No *) ? Yes

 1) Emptying "relation" directory....

 2) Emptying "consensus directory....

 3) Copying "working" to "consensus"....

 4) Creating "relation"....

   Gel Project Disassembled

%

RELATED PROGRAMS

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GelStart begins a fragment assembly session by creating a new fragment assembly project or by identifying an existing project. GelEnter adds fragment sequences to a fragment assembly project. It accepts sequence data from your terminal keyboard, a digitizer, or existing sequence files. GelMerge aligns the sequences in a fragment assembly project into assemblies called contigs. You can view and edit these assemblies in GelAssemble. GelAssemble is a multiple sequence editor for viewing and editing contigs assembled by GelMerge. GelView displays the structure of the contigs in a fragment assembly project. GelDisassemble breaks up the contigs in a fragment assembly project into single fragments.

COMMAND-LINE SUMMARY

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All parameters for this program may be added to the command line. Use -CHEck to view the summary below and to specify parameters before the program executes. In the summary below, the capitalized letters in the parameter names are the letters that you must type in order to use the parameter. Square brackets ([ and ]) enclose parameter values that are optional. For more information, see "Using Program Parameters" in Chapter 3, Using Programs in the User's Guide.


Minimal Syntax: % geldisassemble -Default

Prompted Parameters: None

Local Data Files: None

Optional Parameters:

-ARChive       rebuilds database from the original gel readings
-NOMONitor     suppresses screen monitor of program progress

LOCAL DATA FILES

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None.

PARAMETER REFERENCE

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You can set the parameters listed below from the command line. For more information, see "Using Program Parameters" in Chapter 3, Using Programs in the User's Guide.

-ARChive

rebuilds the database from original gel readings rather than from the working fragments.

-MONitor

This program normally monitors its progress on your screen. However, when you use -Default to suppress all program interaction, you also suppress the monitor. You can turn it back on with this parameter. If you are running the program in batch, the monitor will appear in the log file.

Printed: December 9, 1998 16:26 (1162)

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