MBG 8680: Computer Applications in Molecular Genetics

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FRAGMENT ASSEMBLY SYSTEM


Using GCG to assemble fragments from a sequencing project.

START SEQLAB

telnet to genetics, type gcg, then type seqlab &
Make sure your working dir is set to mbg8680/gcg

CREATE A NEW LIST FILE

Click File, New List, type frags.list, click OK.
Click File, Add Sequences From, Sequence Files.
Select the Frags folder; change the Filter to *
Select all the .frag files, click Add, Close.
Click File, Save List.

START A NEW FAS PROJECT

Click Start.
Select Begin a new project, type project1 for the Name.
Click Run.

ADD THE .FRAG FILES INTO PROJECT1

Click Functions, Fragment Assembly, GelEnter.
Accept "Enter the selected sequences from the Main Window.
Click Run.

MERGE THE FRAGMENTS INTO A CONTIG

Click Functions, Fragment Assembly, GelMerge, Run.
Click Windows, Job Manager, Open Output Mgr
Display the log file.
Close Display, then close Output and Job Manager Windows.

LOAD THE PROJECT1 INTO GELASSEMBLE (MULTIPLE EDITOR)

Click Functions, Fragment Assembly, GelAsseble, Run.
Press Ctrl-K to load contigs.
Press Ctrl-D to start command mode.
Type help for command help.
Type quit to quit GelAssemble.

VIEW THE ASSEMBLED CONTIGS

Click Functions, Fragment Assembly, GelView, Run.
Click Windows, Job Manager, Open Output Mgr
Display the .gelview file.
Close Display, then close Output and Job Manager Windows.

Use the File Manager to explore the various files and folders
under the project1 folder.

Send comments to: dwomble@genetics.wayne.edu

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