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Spanning Disciplines, Advancing Knowledge Promoting Awareness, Progress, and Applications of the Human Genome Project |
Sponsored by the U.S. Department of Energy Human Genome Program
Human
Genome News Archive Edition |
Human Genome News, May 1990; 2(1)
A complete source code distribution of version 1.0 of the gm automated DNA sequence analysis system software is available free of charge to nonprofit laboratories. The gm software identifies all sets of in-frame coding exons separated by introns that satisfy a user-specified set of criteria and translates the exons of each candidate gene to generate a predicted protein sequence. Capable of correctly identifying multiexon genes in 10-kb sequences in a few seconds on a Sun 4 workstation, gm has been tested successfully on sequences of up to 150 kb in length.
This software may be run from a text-only terminal and includes a graphic interface that runs under X-windows (Athena Project, MIT), version 11, release 3, for displaying identified genes and their translation products. C. A. Soderlund, P. Shanmugam, and C. A. Fields of New Mexico State University are developing the automated DNA sequence analysis software with support from the DOE Human Genome Program.
The gm code, written in the C programming language, has been compiled and tested on Sun, Vax, MIPS, Sequent, Silicon Graphics, and Cray computers operating under versions of the Unix operating system. The distribution includes code, documentation, sample input files, and test cases. The code can be obtained either by anonymous file-transfer protocol (ftp) to haywire.nmsu.edu, directory gm, file gm.tar.Z, or by sending a 1/4-inch cartridge tape to Chris Fields, Box 30001/3CRL, New Mexico State University, Las Cruces, NM 88003-0001. Inquiries can also be addressed to cfields@nmsu.edu (internet).
Submitted by C.A. Fields
Computing Research Laboratory
New Mexico State University
(505) 646-2848, Fax: (505) 646-2618
The electronic form of the newsletter may be cited in the following style:
Human Genome Program, U.S. Department of Energy, Human Genome News (v2n1).
Last modified: Wednesday, October 29, 2003
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