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Computer analysis of DNA and protein sequences

European Journal of Biochemistry, 1991
Some recent trends in the development of theoretical methods for DNA and protein sequence analysis are reviewed, with particular emphasis on the design of new databases, motif searches, sequence alignment algorithms and applications of neural networks.
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Computer Manipulation of DNA and Protein Sequences

Current Protocols in Molecular Biology, 1995
AbstractThis unit outlines a variety of methods by which DNA sequences can be manipulated by computers. Procedures for entering sequence data into the computer and assembling raw sequence data into a contiguous sequence are described first, followed by a description of methods of analyzing and manipulating sequences‐‐e.g., verifying sequences ...
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Protein and DNA Sequence Mining

2013
Sequence similarity searching is a method that can be applied by almost anybody for finding similarities between his/her query sequences of amino acids and DNA and the sequences known to be associated with different clinical effects. The latter have been included in database systems like the Basic Local Alignment Search Tool (BLAST) database system ...
Ton J. Cleophas, Aeilko H. Zwinderman
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Sequence-specific interaction of DNA and chromosomal protein

Journal of Molecular Biology, 1969
Abstract The principles which regulate nucleotide sequence-specific binding of chromosomal protein to DNA have been studied with isolated chromatin. The experimental strategy is to dissociate chromosomal proteins from chromatin by 2 m -NaCl and then to determine the conditions under which the chromosomal proteins can be caused to reassociate with ...
I, Bekhor, G M, Kung, J, Bonner
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Sequence Matters: The Influence of Basepair Sequence on DNA-protein Interactions

2007
The sequencing of the human genome, along with the 200-odd other genomes that have been sequenced, does not represent the solution to a puzzle but rather the necessary introduction to a bigger puzzle. That puzzle is how all the 30,000-odd some genes in the human genome are expressed and controlled in a proper sequence for a cell to function.
Yan Mei Wang, Shirley S. Chan, Robert H. Austin   +2 more
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Entropies of coding and noncoding sequences of DNA and proteins

Biophysical Chemistry, 1992
The entropies of protein coding genes from Escherichia coli were calculated according to Boltzmann's formula. Entropies of the coding regions were compared to the entropies of noncoding or miscoding ones. With nucleotides as code units, the entropies of the coding regions, when compared to the entropies of complete sequences (leader and coding region ...
Ilić, Igor, Lauc, Gordan, Heffer, Marija   +2 more
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Indirect Readout of DNA Sequence by Proteins: The Roles of DNA Sequence‐Dependent Intrinsic and Extrinsic Forces

2006
Publisher Summary This chapter discusses the recent insights into how DNA sequence affects DNA structure and how solvent-mediated alterations in DNA structure may play a role in gene regulation. The stability and sequence specificity of many protein–DNA complexes is remarkably dependent on the sequences of bases that are not in contact with protein ...
Gerald B, Koudelka, Steven A, Mauro, Mihai, Ciubotaru   +2 more
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A recurrent DNA sequence at sites of protein interaction

Advances in Biophysics, 1985
Variation in the observed spin lattice relaxation rate (Robs) interpreted as proton exchange dominated in sequences corresponding to part of promoters where RNA polymerase initiates mRNA synthesis has been observed by both Patel et al. and Reid and co-workers.
P, Lu, S, Cheung, M, Donlan
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Identification of Sequence-Specific DNA Binding Proteins

2004
Publisher Summary This chapter describes methods for the identification of nuclear proteins that bind specific DNA sequences within the cis -regulatory domains of genes. Protocols for the preparation of nuclear extract, quantitative electrophoretic mobility shift analysis, oligonucleotide affinity chromatography, and protein preparation for amino ...
James A, Coffman, Chiou-Hwa, Yuh
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Thermodynamics of sequence-specific protein-DNA interactions

Biophysical Chemistry, 1996
The molecular recognition processes in sequence-specific protein-DNA interactions are complex. The only feature common to all sequence-specific protein-DNA structures is a large interaction interface, which displays a high degree of complementarity in terms of shape, polarity and electrostatics.
T, Härd, T, Lundbäck
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