GELSTART

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

FUNCTION

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GelStart begins a fragment assembly session by creating a new fragment assembly project or by identifying an existing 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.

GelStart initializes the fragment assembly environment, locking in the GCG Fragment Assembly System to the project you name. FAS continues to operate on this sequencing project during the current session until you rerun GelStart with a different project name. You must run GelStart each time you use FAS on a different project.

When you name a project, GelStart determines if you are naming a new or existing project. GelStart searches for an existing project of the same name in several places. The order of the search is as follows: 1) the current working directory; 2) a directory defined with the logical name FASPROJECTS; and 3) all of your directories, beginning with the top (or home) directory. (See Chapter 1, Getting Started in the User's Guide for help on defining logical names.) If GelStart finds the project you named, it checks the project database for integrity and then sets the other programs in the fragment assembly package (GelEnter, GelMerge, GelAssemble, GelView and GelDisassemble) to operate on that project. For GelStart to recognize an existing project, it not only must find a root directory with the same name as the project, but also must find the appropriate data subdirectories below the root directory. (See the Introduction to the Fragment Assembly System essay that precedes the FAS program entries in the Program Manual for a more complete description of the fragment assembly database.)

If GelStart does not find the project you have named, it offers to create a new project with that name. New projects are created in your current working directory.

With a new project, GelStart asks if there are any vector sequences that you want highlighted. You can respond with any valid GCG sequence specification. GelEnter then highlights the indicated sequences as you enter them from a digitizer or keyboard. GelMerge reports and optionally excises the indicated sequences from unaligned fragments before it aligns those sequences into assemblies, called contigs. You are not restricted to highlighting only vector sequences. For example, you could specify a fragment that has been over-cloned. GelStart also prompts you to enter any restriction sites that you want highlighted. You must respond with the actual sequence patterns, separated with commas; do not respond with GCG sequence specifications. If you highlight restriction sites, GelEnter can warn you of possible rejoined sticky fragment ends.

EXAMPLE

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Here is a session using GelStart to create a new project named "myproject":


% gelstart

 What is the name of your fragment assembly project?  myproject

 GELSTART cannot find this project. Is it a new one? (* No *)  Yes

 You have a new project named "myproject".

 Which vector sequence(s)would you like highlighted? GB:M13mp18,GB:SynpBR322

 Which restriction site(s) would you like highlighted?  GAATTC,GGATCC

 Project MYPROJECT has 0 fragments in 0 contigs.

 You are ready to run the other fragment assembly programs.

%

OUTPUT

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In this example, you would find a new file in your current working directory named myproject.dir. (See the Introduction to the GCG Fragment Assembly System preceding the FAS program entries in the Program Manual for a more complete description of the fragment assembly database.)

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.

CONSIDERATIONS

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The project name must consist only of characters that can be used in a normal file specification. You cannot have two projects with the same name.

SUGGESTIONS

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You can potentially work on any fragment assembly project by setting your default directory to the directory where the gel project is located. However, make sure that only one person works on the project at a time!

GelStart prompts you for highlighted vector sequences and restriction sites only when you create the project. To reenter or change these specifications, you must use -VECtors and -SITes.

Some of the fragment assembly programs (GelEnter, GelMerge, and GelAssemble) make use of command-line initialization files in the project root directory. For a description of command-line initializing files, see Chapter 3, Using Programs in the User's Guide. If these files don't exist, GelEnter creates them. If a command line initialization file is corrupted, it is best to delete it and allow GelStart to recreate a new one.

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: % gelstart [-NAME=]MyProject -Default

Prompted Parameters:

-NEWproject                       begins a new sequencing project
-VECtors=GB:M13mp18,GB:SynpBR322  highlights specified sequences in GELENTER
-SITes=GAATTC,GGATCC              highlights specified patterns in GELENTER

Local Data Files:  None

Optional Parameters:

-DELete                           deletes a whole project!
-NOMONitor                        suppresses the screen monitor

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.

-NEWproject

creates a new sequencing project if one doesn't already exist with the same name.

-VECtors=GB:M13mp18,GB:SynpBR322

selects vector sequences to highlight when you enter sequences in GelEnter. In GelMerge, you can use -EXCise to remove these vector sequences from the ends of single-fragment contigs.

-SITes=GAATTC,GGATCC

selects patterns to highlight when you enter sequences in GelEnter.

-DELete

deletes a whole project and all of its files. Do not use this parameter unless you want to delete your entire database. Make copies of the sequences you want to save in another directory before using the -DELete option.

-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 16:25 (1162)

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