Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment.
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Summary
A mathematical definition of this "local multiple alignment" problem suitable for full computer automation has been used to develop a new and sensitive algorithm, based on the statistical method of iterative sampling, that finds an optimized local alignment model for N sequences in N-linear time, requiring only seconds on current workstations.
- Type
- article
- Published
- 1993-10-08
- Cited by
- 2,018
- References
- 137
- OpenAlex
- https://openalex.org/W1998300401
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:3040614
Keywords
Computer science, Sequence (biology), Gibbs sampling, Sampling (signal processing), Workstation
References
- Automated assembly of protein blocks for database searching.
- Human brain prostaglandin D synthase has been evolutionarily differentiated from lipophilic-ligand carrier proteins.
- Hierarchical method to align large numbers of biological sequences.
- Local multiple alignment by consensus matrix
- Molecular structure of the bilin binding protein (BBP) from Pieris brassicae after refinement at 2.0 A resolution.
- Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters.
- Definition of general topological equivalence in protein structures. A procedure involving comparison of properties and relationships through simulated annealing and dynamic programming.
- A strategy for the rapid multiple alignment of protein sequences. Confidence levels from tertiary structure comparisons.
- Use of saturation mutagenesis to localize probable functional domains in the NahR protein, a LysR-type transcription activator.
- The helix-turn-helix DNA binding motif.
- The role of the N terminus in Tet repressor for tet operator binding determined by a mutational analysis.
- Flexible protein sequence patterns. A sensitive method to detect weak structural similarities.
- Escherichia coli gene purR encoding a repressor protein for purine nucleotide synthesis. Cloning, nucleotide sequence, and interaction with the purF operator.
- Significance of nucleotide sequence alignments: a method for random sequence permutation that preserves dinucleotide and codon usage.
- A fast and sensitive multiple sequence alignment algorithm
- Trees, stars, and multiple biological sequence alignment
- Profile analysis: detection of distantly related proteins.
- Finding sequence motifs in groups of functionally related proteins.
- Amino acid substitution matrices from an information theoretic perspective
- Pattern recognition in several sequences: consensus and alignment.
Cited by
- Finding Transcription Factor Binding Sites in Coregulated Genes by Exhaustive Sequence Search
- Classification of genes using probabilistic models of microarray expression profiles
- Coordinate positioning of MEF2 and myogenin binding sites.
- Hidden Markov models for sequence analysis: extension and analysis of the basic method
- Self‐organizing hierarchic networks for pattern recognition in protein sequence
- Extracting protein alignment models from the sequence database.
- A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K-12 genome.
- Family pairwise search with embedded motif models
- Evaluation Measures of Multiple Sequence Alignments
- The current excitement in bioinformatics-analysis of whole-genome expression data: how does it relate to protein structure and function?
- Surveying Saccharomyces genomes to identify functional elements by comparative DNA sequence analysis.
- Probabilistic prediction of Saccharomyces cerevisiae mRNA 3'-processing sites.
- Whole-genome discovery of transcription factor binding sites by network-level conservation.
- Segment-Based Scores for Pairwise and Multiple Sequence Alignments
- Automatic annotation of protein motif function with Gene Ontology terms
- Conservative extraction of over-represented extensible motifs
- Reliable prediction of transcription factor binding sites by phylogenetic verification.
- Synthetic promoters: genetic control through cis engineering.
- Structural and evolutionary bioinformatics of the SPOUT superfamily of methyltransferases
- Connecting protein structure with predictions of regulatory sites
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