Bioinformatics Resources
Molecular & Genetic Bioinformatics Facility

Faculty – available for consulting & training

Databases and Software

Sequence Analysis At UAB

 

Biological Computing Resource Facility
Where you get help

DIRECTOR:

 Elliot Lefkowitz, Ph.D., Department of Microbiology

Office:

 BBRB 277A

Phone:

 (205) 934-1946

E-mail:

 ElliotL@uab.edu

WEB SITE:

 http://www.genome.uab.edu
Analyze
The Sun UNIX Computer of the Molecular & Genetic Bioinformatics Resource
Internet Address: gcg.genome.uab.edu

The Genetics Computer Group (GCG)
Sequence Analysis Software Package

Required Hardware and Software

Using UNIX

Logging On

Command-line Syntax

analyze> command -PARameter

Line editing commands

Delete (or Backspace) Key
Delete the character to the left of the cursor
 
Long Commands
At the end of the line type a backslash (\) and hit return
To Replay a previous command
analyze> history
Shows you the commands you have previously issued
To replay command number 5:
analyze> !5

Help

analyze> man command_name
Displays online documentation about the command
 
analyze> man -k list
Displays all commands that relate to the word list

File and Directory Specifications

Wild Cards

* Any number of any character;

? Any single character

Control Keys

ctrl-c ends a program (ctrl-y on orion)

ctrl-d end of a file (ctrl-z on the orion)

UNIX Commands

General

logout
Finished. I want to go home.
 
passwd
Change your password

Directory Manipulation

ls
List the files in the current directory
 
analyze> ls seqs
List all the files in the subdirectory named seqs
ls -l
provides more information in the listing
 
ls -lt
sorts the listing by date
 
cd directory_name
Change to the directory_name directory
 
cd ..
Go up one directory
 
up (GCG Command)
Go to the directory one up from my current directory
 
down directory_name (GCG Command)
Go down to the directory_name directory
 
home
Take me to my login directory
 
mkdir directory_name
Creates a new subdirectory in the current directory
 
rmdir directory_name
deletes a directory
 
pwd
Where am I?

File Handling

cp filename1 filename2
Create a copy of a filename1 (and call it filename2)
 
rm filename
Deletes a file
 
mv filename1 filename2
Changes the file name
 
grep 'character_pattern' filename(s)
find the lines in filename(s) that match the pattern

Text Output

cat filename
List the file to the screen
 
more filename
List the file to the screen one page at a time
 

Using GCG

Getting Started

Initialize the GCG Programs
analyze> gcg
(If not already done)
Help
http://www.genome.uab.edu/GCG/help/
 
While on analyze:
analyze> genhelp
On-line help arranged by program
 
analyze> genmanual
On-line Manual

Copying Data or Sequence Files

analyze>fetch enzyme.dat
(Restriction enzyme list)
 
analyze> fetch GE:vsvcg
(The Genbank sequence for vsvcg)

Displaying Data or Sequence Files

analyze> typedata Enzyme.dat
Display the data and documentation
 
analyze> typedata -ref GE:vsvcg
Display documentation only

Running Programs

Programs

  • Type the name of the program
  • Do not abbreviate program names
  • Program names are case sensitive

Program Parameters

  • A dash (-) indicates a program parameter
  • Parameters can be abbreviated
  • Parameters are case insensitive
Global Switches
Changes your GCG environment
Type at the analyze> prompt
doc
Displays a short paragraph describing the program being run
 
nodoc
Suppresses the documentation displayed for each GCG program
 
comcheck
Displays a list of command line options when a program is run
Gives you a chance to enter new options after you have started a program
 
nocomcheck
Turns the ComCheck option off.

General Program Switches

  • Enter on the command line following the program name
  • Enter at the program prompt if -Check or ComCheck is active
-DEFault
use default values for every parameter not indicated on the command line
-PROtein
sets the program to expect protein sequences.
-NOPROtein
insists that your sequences are nucleic acids.
-CHEck
prints a summary of the available command line parameters

Cutting Computer Costs

Expensive programs (run automatically in batch mode)

BLAST, Compare, FastA, FindPatterns, FoldRNA, FrameAlign, FrameSearch, GelMerge, MFold, PileUp, Prime, ProfileSearch, StringSearch, TFastA, WordSearch

Batch jobs

  • The program will prompt you for required information
  • The program is automatically submitted to a batch queue
  • Use -NOBatch if you do not want to use batch mode

Graphic Output

You must first specify a graphic device before running a program.
analyze> setplot

PostScript Output

  • Create a PostScript text file
  • Choose the Postscript option from SetPlot
  • A postscript graphic file will be created
  • Send the PostScript file to your computer
    (Use FTP)
  • Send the PostScript file to your Laser Printer
  • Use the Apple LaserWriter Utility or another program that will download postscript files to a postscript printer

SeqLab

analyze> seqlab &

  • Launches the Xwndows interface for running GCG programs
  • Must be running an Xwindows package (like Exodus) on your Mac or PC

 

Support for these Bioinformatics Resources is provided by the UAB
Center for AIDS Research · Comprehensive Cancer Center · Health Services Foundation