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III. Molecular Biology software tools

***This course will cover three basic types of software tools for molecular biology computing.

***The primary emphasis will be equally divided between the GCG package (which runs on the RCR's server) and on information and computing resources that are freely available over the World Wide Web

*** A minor emphasis will be on software for personal computers (with a bias toward Macintosh computers)


A. GCG

***The primary application that the RCR provides to the Medical Center is GCG, the Wisconsin Sequence Analysis Package which runs on our Alpha server under the UNIX operating system.

***GCG is the most popular and most comprehensive set of tools for the molecular biologist 

GCG is a comprehensive suite of molecular biology tools that offers
everything from database searching, multiple alignment, sequence 
editing and assembly (for sequencing projects), to protein and RNA 
3D structural analysis. All of the tools in GCG have a similar 
interface and they are designed to work together in the sense that 
the output of one program can be used as input for the next.
***It is necessary for users to have a rudimentary knowledge of the UNIX operating system in order to use GCG. We will cover some basic UNIX commands for dealing with files and directories and editing text documents in the next two lectures.

***The GCG package also has an X-Windows interface (SeqLab) and a brand new web interface called SeqWeb. We will work with the traditional text interface to GCG first because it will give you more power and more insight into the inner workings of the program, but I expect that within a few months or years, everyone will use GCG over the web exclusively.

B. Macintosh/PC Programs

***The RCR provides site licenses to its members for several molecular biology packages for personal computers:

***Macintosh programs
  • MacVector
  • Sequencher (DNA sequenceing)

*** Windows programs
  • OMIGA
  • Sequencher (DNA sequenceing)
***The RCR also maintains an archive of current versions of molecular biology related shareware/freeware programs and demo versions of commercial programs:

http://endeavor.med.nyu.edu/download/molbio/
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Using Computers for Molecular Biology
Stuart M. Brown, Ph.D., RCR, NYU Medical Center
Comments to: browns02@mcrcr.med.nyu.edu