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Aligning a DNA sequence with a protein sequence
Proceedings of the first annual international conference on Computational molecular biology - RECOMB '97, 1997We develop several algorithms for the problem of aligning DNA sequence with a protein sequence. Our methods account for frameshift errors, but not for introns in the DNA sequence. Thus, they are particularly appropriate for comparing a cDNA sequence that suffers from sequencing errors with an amino acid sequence or a protein sequence database.
Zheng Zhang 0004 +2 more
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Analytical Biochemistry, 1994
DNA sequencing technology was modified into a quantitative assay, which for multiple DNA sequences allowed the simultaneous determination of relative protein-DNA binding constants. The band mobility shift of the protein-DNA binding reactions partitions the mixture of DNA sequences into bound and unbound fractions.
D S, Fields, G D, Stormo
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DNA sequencing technology was modified into a quantitative assay, which for multiple DNA sequences allowed the simultaneous determination of relative protein-DNA binding constants. The band mobility shift of the protein-DNA binding reactions partitions the mixture of DNA sequences into bound and unbound fractions.
D S, Fields, G D, Stormo
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Fast Comparison of a DNA Sequence with a Protein Sequence Database
Genome Science and Technology, 1996We describe a computer program, named DNA-Protein Search (DPS), for comparing a megabase DNA sequence with a protein sequence database. The DPS program addresses the problems of frameshifts and introns in the DNA sequence. The DPS program was used to compare each of the following sequences with the Swiss-Prot database: the 1.8-megabase sequence of the ...
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Computer analysis of DNA and protein sequences
European Journal of Biochemistry, 1991Some 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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Aligning DNA Sequences to Minimize the Change in Protein
Journal of Combinatorial Optimization, 1999zbMATH Open Web Interface contents unavailable due to conflicting licenses.
Yufang Hua, Tao Jiang 0001, Bin Wu
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Computer Manipulation of DNA and Protein Sequences
Current Protocols in Molecular Biology, 1995AbstractThis 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
2013Sequence 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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Statistical Methods and Insights for Protein and DNA Sequences
Annual Review of Biophysics and Biophysical Chemistry, 1991Note: Department of Mathematics, Stanford University, California 94305.
S, Karlin +3 more
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Entropies of coding and noncoding sequences of DNA and proteins
Biophysical Chemistry, 1992The 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 +2 more
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Sequence-specific interaction of DNA and chromosomal protein
Journal of Molecular Biology, 1969Abstract 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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