GELVIEW

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

FUNCTION

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GelView displays the structure of the contigs in a fragment assembly project.

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.

GelView makes a display of your fragment assembly project. A list of the fragments in each contig, along with a bar diagram representing the position, length, and orientation of each fragment, allows you to review the current status of your sequencing project.

EXAMPLE

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Here is a session using GelView to look at the contigs in "myproject." This project was created in the example sessions of GelStart, GelEnter, and GelMerge.


% gelview

 What should I call the output file (* myproject.view *) ?

 MYPROJECT has 12 Fragments in 3 Contigs

%

OUTPUT

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GELVIEW Fragment Assembly contig display of Project: myproject
    September 24, 1998 09:05

Contig: mu2

   3       mu23        +--------------------------->
   2       mu2         +----------------------------------->
   C       CONSENSUS   +----------------------------------->
                       |----------|----------|----------|---------|---------|
                       0         100        200        300        400

Contig: mu26b

   8       mu18b                              +--------------------->
   7       mu9                            <---+
   6       mu32                          +--->
   5       mu26                          <----+
   4       mu18                          +---->
   3       mu27                       <--------------------------------+
   2       mu26b       <------------------+
   C       CONSENSUS   <-----------------------------------------------+
                       |----------|----------|----------|---------|---------|
                       0         100        200        300        400

Contig: mu5

   4       mu6                     <--------------------------------+
   3       mu10        +--------------------------------------->
   2       mu5         <------------------------+
   C       CONSENSUS   <--------------------------------------------+
                       |----------|----------|----------|---------|---------|
                       0         100        200        300        400

 12 Fragments in 3 Contigs

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.

RESTRICTIONS

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A contig may not contain more than 1,650 fragments and may not be longer than 200,000 bases. No single fragment may be longer than 2,500 bases.

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: % gelview -Default

Prompted Parameters:

[-OUTfile=]myproject.view   names the output file

Local Data Files: None

Optional Parameters:

-NOBAR                      suppresses the fragment bar diagrams

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.

-NOBAR

suppresses the bar diagram associated with each fragment name.

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

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