Gene recognition and assembly in the GRAIL system: Progress and challenges
- Oak Ridge National Lab., Oak Ridge, TN (United States)
GRAIL is a comprehensive system being constructed to analyze and characterize the genetic structure of DNA sequences. A number of program modules supply information to the system including the Coding Recognition Module (CRM), which forms the basis of the current e-mail GRAIL server system. Additional modules determine the positions and scores of possible splice junctions, the positions of potential translation-initiation sites, the coding strand for each gene, and the probable-translation-frame function over the sequence. The Gene Assembly Program module (GAP) attempts to predict the sequence of the spliced MRNA for a gene from the genomic DNA sequence. It constructs and scores gene models, given a DNA sequence and the outputs of the other GRAIL modules for the sequence. GAP tests combinations of those splice junctions which are within acceptable distance from the initial predicted edges of the coding regions. Every complete gene model, comprising translation-initiation site, splice junctions and stop codon, which agrees with GAP`s set of rules is scored, and the ten highest-scoring models are saved. Each gene model`s score depends on the input scores of splice junctions used in the model, their positions relative to the initial predicted edges of the included coding regions, and the degree of agreement of the entire model with the probable-translation-frame function. If error conditions are detected, the present version of GAP attempts to correct them by the insertion and/or deletion of one or more coding regions.
- DOE Contract Number:
- AC05-84OR21400
- OSTI ID:
- 37553
- Report Number(s):
- CONF-9206273-; ISBN 981-02-1157-0; TRN: IM9519%%479
- Resource Relation:
- Conference: 2. international conference on bioinformatics, supercomputing, and complex genome analysis, St. Petersburg, FL (United States), 4-7 Jun 1992; Other Information: PBD: 1993; Related Information: Is Part Of The second international conference on bioinformatics, supercomputing and complex genome analysis; Lim, H.A. [ed.] [Florida State Univ., Tallahassee, FL (United States). Supercomputer Computations Research Inst.]; Fickett, J.W. [ed.] [Los Alamos National Lab., Los Alamos, NM (United States). Center for Human Genome Studies]; Cantor, C.R. [ed.] [Boston Univ., MA (United States). Center for Advanced Research in Biotechnology]; Robbins, R.J. [ed.] [Johns Hopkins Univ., Baltimore, MD (United States). Applied Research Lab.]; PB: 672 p.
- Country of Publication:
- United States
- Language:
- English
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