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© IRL Press at Oxford University Press

gm: a practical tool for automating DNA sequence analysis

C.A. Fields 1,* and C.A. Soderlund 1,2

1Center for Advanced Computing in Molecular and Cellular Biology, Computing Research Laboratory Box 3000I/3CRL
2Department of Computer Science Box 3000I/3CV, New Mexico State University, Las Cruces, NM 88003-0001, USA

*To whom reprint requests should be sent

The gm (gene modeler) program automates the identification of candidate genes in anonymous, genomic DNA sequence data, gm accepts sequence data, organism-specific consensus matrices and codon asymmetry tables, and a set of parameters as input; it returns a set of models describing the structures of candidate genes in the sequence and a corresponding set of predicted amino acid sequences as output, gm is implemented in C, and has been tested on Sun, VAX, Sequent, MIPS and Cray computers. It is capable of analyzing sequences of several kilobases containing multi-exon genes in >1 min execution time on a Sun 4/60.

Received on December 4, 1989; accepted on February 28, 1990

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