Searching for Genes

The collecting, organizing and indexing of sequence information into a database, a challenging task in itself, provides the scientist with a wealth of information, albeit of limited use. The power of a database comes not from the collection of information, but in its analysis. A sequence of DNA does not necessarily constitute a gene. It may constitute only a fragment of a gene or alternatively, it may contain several genes.

Luckily, in agreement with evolutionary principles, scientific research to date has shown that all genes share common elements. For many genetic elements, it has been possible to construct consensus sequences, those sequences best representing the norm for a given class of organisms (e.g, bacteria, eukaroytes). Common genetic elements include promoters, enhancers, polyadenylation signal sequences and protein binding sites. These elements have also been further characterized into further subelements.

Genetic elements share common sequences, and it is this fact that allows mathematical algorithms to be applied to the analysis of sequence data. A computer program for finding genes will contain at least the following elements.

Elements of a Gene-seeking Computer Program

Algorithms for pattern recognition Probability formulae are used to determine if two sequences are statistically similar.
Data Tables These tables contain information on consensus sequences for various genetic elements. More information enables a better analysis.
Taxonomic Differences Consensus sequences vary between different taxonomic classes of organisms. Inclusion of these differences in an analysis speeds processing and minimizes error.
Analysis rules These programming instructions define how algorithms are applied. They define the degree of similarity accepted and whether entire sequences and/or fragments thereof will be considered in the analysis. A good program design enables users to adjust these variables.

Last updated: July 23, 1998
URL: http://biotech.icmb.utexas.edu/pages/bioinform/BIgenes.html
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Elements of a Gene-seeking Computer Program
Algorithms for pattern recognition	Probability formulae are used to determine if two sequences are statistically similar.
Data Tables	These tables contain information on consensus sequences for various genetic elements. More information enables a better analysis.
Taxonomic Differences	Consensus sequences vary between different taxonomic classes of organisms. Inclusion of these differences in an analysis speeds processing and minimizes error.
Analysis rules	These programming instructions define how algorithms are applied. They define the degree of similarity accepted and whether entire sequences and/or fragments thereof will be considered in the analysis. A good program design enables users to adjust these variables.