Combinatorial approaches to gene recognition

Recognition of genes via exon assembly approaches leads naturally to the use of dynamic programming. We consider the general graph-theoretical formulation of the exon assembly problem and analyze in detail some specific variants: multicriterial optimization in the case of non-linear gene-scoring fun...

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Bibliographic Details
Published in:Computers & chemistry 1997-01, Vol.21 (4), p.229-235
Main Authors: Roytberg, M.A., Astakhova, T.V., Gelfand, M.S.
Format: Article
Language:English
Subjects:
Base Sequence
DNA - chemistry
DNA - genetics
DNA Primers
Exons
Genetic Techniques
Mathematics
Models, Genetic
Molecular Sequence Data
Oligonucleotide Probes
Polymerase Chain Reaction
Reading Frames
Software
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Summary:Recognition of genes via exon assembly approaches leads naturally to the use of dynamic programming. We consider the general graph-theoretical formulation of the exon assembly problem and analyze in detail some specific variants: multicriterial optimization in the case of non-linear gene-scoring functions; context-dependent schemes for scoring exons and related procedures for exon filtering; and highly specific recognition of arbitrary gene segments, oligonucleotide probes and polymerase chain reaction (PCR) primers. ‡ ‡ Described programs are available at http://wwww-hto.usc.edu/software/procrustes/
ISSN:0097-8485
DOI:10.1016/S0097-8485(96)00034-4