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Multiple sequence alignment: algorithms and applications
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scholarly article
1 reference
stated in
Europe PubMed Central
PubMed ID
10463075
retrieved
28 July 2017
review article
1 reference
stated in
Europe PubMed Central
title
Multiple sequence alignment: algorithms and applications
(English)
1 reference
stated in
Europe PubMed Central
PubMed ID
10463075
retrieved
28 July 2017
main subject
sequence alignment
1 reference
based on heuristic
inferred from title
algorithm
0 references
author name string
Gotoh O
series ordinal
1
1 reference
stated in
Europe PubMed Central
PubMed ID
10463075
retrieved
28 July 2017
publication date
1 January 1999
1 reference
stated in
Europe PubMed Central
PubMed ID
10463075
retrieved
28 July 2017
published in
Advances in Biophysics
1 reference
stated in
Europe PubMed Central
PubMed ID
10463075
retrieved
28 July 2017
volume
36
1 reference
stated in
Europe PubMed Central
PubMed ID
10463075
retrieved
28 July 2017
page(s)
159-206
1 reference
stated in
Europe PubMed Central
PubMed ID
10463075
retrieved
28 July 2017
cites work
Analysis of amino acid indices and mutation matrices for sequence comparison and structure prediction of proteins
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Exhaustive matching of the entire protein sequence database
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An Assessment of Amino Acid Exchange Matrices in Aligning Protein Sequences: The Twilight Zone Revisited
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Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed by reference to structural alignments
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Analysis of insertions/deletions in protein structures
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Sensitivity and selectivity in protein similarity searches: a comparison of Smith-Waterman in hardware to BLAST and FASTA.
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Empirical and structural models for insertions and deletions in the divergent evolution of proteins.
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A general method applicable to the search for similarities in the amino acid sequence of two proteins
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The theory and computation of evolutionary distances: Pattern recognition
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7 January 2021
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Some biological sequence metrics
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Crossref
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7 January 2021
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Comparative biosequence metrics
1 reference
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7 January 2021
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On the Theory and Computation of Evolutionary Distances
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7 January 2021
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The String-to-String Correction Problem
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7 January 2021
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An improved algorithm for matching biological sequences.
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7 January 2021
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Optimal sequence alignment allowing for long gaps.
1 reference
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7 January 2021
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Sequence comparison with concave weighting functions.
1 reference
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7 January 2021
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Finite-state models in the alignment of macromolecules
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7 January 2021
based on heuristic
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Optimal sequence alignment using affine gap costs
1 reference
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7 January 2021
based on heuristic
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A fast homology program for aligning biological sequences.
1 reference
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Crossref
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7 January 2021
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Recent developments in linear-space alignment methods: a survey.
1 reference
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7 January 2021
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Suboptimal sequence alignment in molecular biology
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7 January 2021
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Minimal Mutation Trees of Sequences
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Crossref
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7 January 2021
based on heuristic
inferred from DOI database lookup
Gap costs for multiple sequence alignment
1 reference
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Crossref
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7 January 2021
based on heuristic
inferred from DOI database lookup
Alignment of three biological sequences with an efficient traceback procedure
1 reference
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Crossref
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7 January 2021
based on heuristic
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Frequency of insertion-deletion, transversion, and transition in the evolution of 5S ribosomal RNA
1 reference
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Crossref
reference URL
https://api.crossref.org/works/10.1016%2FS0065-227X%2899%2980007-0
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7 January 2021
based on heuristic
inferred from DOI database lookup
Fast optimal alignment
1 reference
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Crossref
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7 January 2021
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Algorithms for approximate string matching
1 reference
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Crossref
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7 January 2021
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The Multiple Sequence Alignment Problem in Biology
1 reference
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7 January 2021
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A Formal Basis for the Heuristic Determination of Minimum Cost Paths
1 reference
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7 January 2021
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Improving the practical space and time efficiency of the shortest-paths approach to sum-of-pairs multiple sequence alignment.
1 reference
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7 January 2021
based on heuristic
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A multiple sequence alignment program
1 reference
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Crossref
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7 January 2021
based on heuristic
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Efficient algorithms for folding and comparing nucleic acid sequences
1 reference
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Crossref
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7 January 2021
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A workbench for multiple alignment construction and analysis
1 reference
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Crossref
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7 January 2021
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An interactive graphics program for comparing and aligning nucleic acid and amino acid sequences
1 reference
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Crossref
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7 January 2021
based on heuristic
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Motif recognition and alignment for many sequences by comparison of dot-matrices.
1 reference
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Crossref
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7 January 2021
based on heuristic
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A method for the simultaneous alignment of three or more amino acid sequences.
1 reference
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Crossref
reference URL
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7 January 2021
based on heuristic
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Multiple sequence alignment by consensus
1 reference
stated in
Crossref
reference URL
https://api.crossref.org/works/10.1016%2FS0065-227X%2899%2980007-0
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7 January 2021
based on heuristic
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Consistency of optimal sequence alignments
1 reference
stated in
Crossref
reference URL
https://api.crossref.org/works/10.1016%2FS0065-227X%2899%2980007-0
retrieved
7 January 2021
based on heuristic
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Determination of reliable regions in protein sequence alignments
1 reference
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Crossref
reference URL
https://api.crossref.org/works/10.1016%2FS0065-227X%2899%2980007-0
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7 January 2021
based on heuristic
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Quantifying the local reliability of a sequence alignment.
1 reference
stated in
Crossref
reference URL
https://api.crossref.org/works/10.1016%2FS0065-227X%2899%2980007-0
retrieved
7 January 2021
based on heuristic
inferred from DOI database lookup
Maximum likelihood alignment of DNA sequences
1 reference
stated in
Crossref
reference URL
https://api.crossref.org/works/10.1016%2FS0065-227X%2899%2980007-0
retrieved
7 January 2021
based on heuristic
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An evolutionary model for maximum likelihood alignment of DNA sequences
1 reference
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Crossref
reference URL
https://api.crossref.org/works/10.1016%2FS0065-227X%2899%2980007-0
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7 January 2021
based on heuristic
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Inching toward reality: an improved likelihood model of sequence evolution
1 reference
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Crossref
reference URL
https://api.crossref.org/works/10.1016%2FS0065-227X%2899%2980007-0
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7 January 2021
based on heuristic
inferred from DOI database lookup
Alignment of molecular sequences seen as random path analysis
1 reference
stated in
Crossref
reference URL
https://api.crossref.org/works/10.1016%2FS0065-227X%2899%2980007-0
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7 January 2021
based on heuristic
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A reliable sequence alignment method based on probabilities of residue correspondences.
1 reference
stated in
Crossref
reference URL
https://api.crossref.org/works/10.1016%2FS0065-227X%2899%2980007-0
retrieved
7 January 2021
based on heuristic
inferred from DOI database lookup
A general method for fast multiple sequence alignment.
1 reference
stated in
Crossref
reference URL
https://api.crossref.org/works/10.1016%2FS0065-227X%2899%2980007-0
retrieved
7 January 2021
based on heuristic
inferred from DOI database lookup
Multiple sequence alignment with the Divide-and-Conquer method
1 reference
stated in
Crossref
reference URL
https://api.crossref.org/works/10.1016%2FS0065-227X%2899%2980007-0
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7 January 2021
based on heuristic
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The alignment of sets of sequences and the construction of phyletic trees: an integrated method
1 reference
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Crossref
reference URL
https://api.crossref.org/works/10.1016%2FS0065-227X%2899%2980007-0
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7 January 2021
based on heuristic
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Progressive sequence alignment as a prerequisite to correct phylogenetic trees
1 reference
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Crossref
reference URL
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7 January 2021
based on heuristic
inferred from DOI database lookup
A flexible method to align large numbers of biological sequences.
1 reference
stated in
Crossref
reference URL
https://api.crossref.org/works/10.1016%2FS0065-227X%2899%2980007-0
retrieved
7 January 2021
based on heuristic
inferred from DOI database lookup
A strategy for the rapid multiple alignment of protein sequences. Confidence levels from tertiary structure comparisons
1 reference
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Crossref
reference URL
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retrieved
7 January 2021
based on heuristic
inferred from DOI database lookup
Multiple sequence alignment with hierarchical clustering
1 reference
stated in
Crossref
reference URL
https://api.crossref.org/works/10.1016%2FS0065-227X%2899%2980007-0
retrieved
7 January 2021
based on heuristic
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A survey of multiple sequence comparison methods
1 reference
stated in
Crossref
reference URL
https://api.crossref.org/works/10.1016%2FS0065-227X%2899%2980007-0
retrieved
7 January 2021
based on heuristic
inferred from DOI database lookup
Progressive alignment of amino acid sequences and construction of phylogenetic trees from them
1 reference
stated in
Crossref
reference URL
https://api.crossref.org/works/10.1016%2FS0065-227X%2899%2980007-0
retrieved
7 January 2021
based on heuristic
inferred from DOI database lookup
Using CLUSTAL for multiple sequence alignments
1 reference
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Crossref
reference URL
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7 January 2021
based on heuristic
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Computational space reduction and parallelization of a new clustering approach for large groups of sequences
1 reference
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reference URL
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7 January 2021
based on heuristic
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MULTAN: a program to align multiple DNA sequences
1 reference
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reference URL
https://api.crossref.org/works/10.1016%2FS0065-227X%2899%2980007-0
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7 January 2021
based on heuristic
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CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
1 reference
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Crossref
reference URL
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7 January 2021
based on heuristic
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An investigation of conservation-biased gap-penalties for multiple protein sequence alignment.
1 reference
stated in
Crossref
reference URL
https://api.crossref.org/works/10.1016%2FS0065-227X%2899%2980007-0
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7 January 2021
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Hidden Markov models in computational biology. Applications to protein modeling
1 reference
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reference URL
https://api.crossref.org/works/10.1016%2FS0065-227X%2899%2980007-0
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7 January 2021
based on heuristic
inferred from DOI database lookup
A method for multiple sequence alignment with gaps.
1 reference
stated in
Crossref
reference URL
https://api.crossref.org/works/10.1016%2FS0065-227X%2899%2980007-0
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7 January 2021
based on heuristic
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Weights for data related by a tree
1 reference
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Crossref
reference URL
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7 January 2021
based on heuristic
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Optimization by Simulated Annealing
1 reference
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reference URL
https://api.crossref.org/works/10.1016%2FS0065-227X%2899%2980007-0
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7 January 2021
based on heuristic
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Multiple alignment using simulated annealing: branch point definition in human mRNA splicing
1 reference
stated in
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reference URL
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7 January 2021
based on heuristic
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Definition of general topological equivalence in protein structures. A procedure involving comparison of properties and relationships through simulated annealing and dynamic programming
1 reference
stated in
Crossref
reference URL
https://api.crossref.org/works/10.1016%2FS0065-227X%2899%2980007-0
retrieved
7 January 2021
based on heuristic
inferred from DOI database lookup
Protein structure comparison by alignment of distance matrices
1 reference
stated in
Crossref
reference URL
https://api.crossref.org/works/10.1016%2FS0065-227X%2899%2980007-0
retrieved
7 January 2021
based on heuristic
inferred from DOI database lookup
Alignment and searching for common protein folds using a data bank of structural templates
1 reference
stated in
Crossref
reference URL
https://api.crossref.org/works/10.1016%2FS0065-227X%2899%2980007-0
retrieved
7 January 2021
based on heuristic
inferred from DOI database lookup
SAGA: sequence alignment by genetic algorithm
1 reference
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Crossref
reference URL
https://api.crossref.org/works/10.1016%2FS0065-227X%2899%2980007-0
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7 January 2021
based on heuristic
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RAGA: RNA sequence alignment by genetic algorithm
1 reference
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Crossref
reference URL
https://api.crossref.org/works/10.1016%2FS0065-227X%2899%2980007-0
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7 January 2021
based on heuristic
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COFFEE: an objective function for multiple sequence alignments
1 reference
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Crossref
reference URL
https://api.crossref.org/works/10.1016%2FS0065-227X%2899%2980007-0
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7 January 2021
based on heuristic
inferred from DOI database lookup
Identification of common molecular subsequences
1 reference
stated in
Crossref
reference URL
https://api.crossref.org/works/10.1016%2FS0065-227X%2899%2980007-0
retrieved
7 January 2021
based on heuristic
inferred from DOI database lookup
Pattern recognition in nucleic acid sequences. I. A general method for finding local homologies and symmetries
1 reference
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Crossref
reference URL
https://api.crossref.org/works/10.1016%2FS0065-227X%2899%2980007-0
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7 January 2021
based on heuristic
inferred from DOI database lookup
Derivation of rules for comparative protein modeling from a database of protein structure alignments
1 reference
stated in
Crossref
reference URL
https://api.crossref.org/works/10.1016%2FS0065-227X%2899%2980007-0
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7 January 2021
based on heuristic
inferred from DOI database lookup
A databank (3D-ali) collecting related protein sequences and structures
1 reference
stated in
Crossref
reference URL
https://api.crossref.org/works/10.1016%2FS0065-227X%2899%2980007-0
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7 January 2021
based on heuristic
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The FSSP database: fold classification based on structure-structure alignment of proteins
1 reference
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Crossref
reference URL
https://api.crossref.org/works/10.1016%2FS0065-227X%2899%2980007-0
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7 January 2021
based on heuristic
inferred from DOI database lookup
HOMSTRAD: a database of protein structure alignments for homologous families
1 reference
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Crossref
reference URL
https://api.crossref.org/works/10.1016%2FS0065-227X%2899%2980007-0
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7 January 2021
based on heuristic
inferred from DOI database lookup
CAMPASS: a database of structurally aligned protein superfamilies.
1 reference
stated in
Crossref
reference URL
https://api.crossref.org/works/10.1016%2FS0065-227X%2899%2980007-0
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7 January 2021
based on heuristic
inferred from DOI database lookup
The structural alignment between two proteins: is there a unique answer?
1 reference
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Crossref
reference URL
https://api.crossref.org/works/10.1016%2FS0065-227X%2899%2980007-0
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7 January 2021
based on heuristic
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Comparative analysis of seven multiple protein sequence alignment servers: clues to enhance reliability of predictions
1 reference
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Crossref
reference URL
https://api.crossref.org/works/10.1016%2FS0065-227X%2899%2980007-0
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7 January 2021
based on heuristic
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Prediction of protein secondary structure at better than 70% accuracy
1 reference
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Crossref
reference URL
https://api.crossref.org/works/10.1016%2FS0065-227X%2899%2980007-0
retrieved
7 January 2021
based on heuristic
inferred from DOI database lookup
Identification and application of the concepts important for accurate and reliable protein secondary structure prediction
1 reference
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Crossref
reference URL
https://api.crossref.org/works/10.1016%2FS0065-227X%2899%2980007-0
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7 January 2021
based on heuristic
inferred from DOI database lookup
The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools
1 reference
stated in
Crossref
reference URL
https://api.crossref.org/works/10.1016%2FS0065-227X%2899%2980007-0
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7 January 2021
based on heuristic
inferred from DOI database lookup
A symmetric-iterated multiple alignment of protein sequences.
1 reference
stated in
Crossref
reference URL
https://api.crossref.org/works/10.1016%2FS0065-227X%2899%2980007-0
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7 January 2021
based on heuristic
inferred from DOI database lookup
Phylogenies from molecular sequences: inference and reliability
1 reference
stated in
Crossref
reference URL
https://api.crossref.org/works/10.1016%2FS0065-227X%2899%2980007-0
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7 January 2021
based on heuristic
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Phylogenetic analysis in molecular evolutionary genetics
1 reference
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Crossref
reference URL
https://api.crossref.org/works/10.1016%2FS0065-227X%2899%2980007-0
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7 January 2021
based on heuristic
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Reconstruction of gene trees from sequence data
1 reference
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Crossref
reference URL
https://api.crossref.org/works/10.1016%2FS0065-227X%2899%2980007-0
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7 January 2021
based on heuristic
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Effects of nucleotide sequence alignment on phylogeny estimation: a case study of 18S rDNAs of apicomplexa
1 reference
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Crossref
reference URL
https://api.crossref.org/works/10.1016%2FS0065-227X%2899%2980007-0
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7 January 2021
based on heuristic
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Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods
1 reference
stated in
Crossref
reference URL
https://api.crossref.org/works/10.1016%2FS0065-227X%2899%2980007-0
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7 January 2021
based on heuristic
inferred from DOI database lookup
The posterior probability distribution of alignments and its application to parameter estimation of evolutionary trees and to optimization of multiple alignments.
1 reference
stated in
Crossref
reference URL
https://api.crossref.org/works/10.1016%2FS0065-227X%2899%2980007-0
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7 January 2021
based on heuristic
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Predicting functions from protein sequences--where are the bottlenecks?
1 reference
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reference URL
https://api.crossref.org/works/10.1016%2FS0065-227X%2899%2980007-0
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7 January 2021
based on heuristic
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Functional genomics--bioinformatics is ready for the challenge
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7 January 2021
based on heuristic
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Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods
1 reference
stated in
Crossref
reference URL
https://api.crossref.org/works/10.1016%2FS0065-227X%2899%2980007-0
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7 January 2021
based on heuristic
inferred from DOI database lookup
Recognition of related proteins by iterative template refinement (ITR)
1 reference
stated in
Crossref
reference URL
https://api.crossref.org/works/10.1016%2FS0065-227X%2899%2980007-0
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7 January 2021
based on heuristic
inferred from DOI database lookup
Extracting protein alignment models from the sequence database
1 reference
stated in
Crossref
reference URL
https://api.crossref.org/works/10.1016%2FS0065-227X%2899%2980007-0
retrieved
7 January 2021
based on heuristic
inferred from DOI database lookup
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
1 reference
stated in
Crossref
reference URL
https://api.crossref.org/works/10.1016%2FS0065-227X%2899%2980007-0
retrieved
7 January 2021
based on heuristic
inferred from DOI database lookup
Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection
1 reference
stated in
Crossref
reference URL
https://api.crossref.org/works/10.1016%2FS0065-227X%2899%2980007-0
retrieved
7 January 2021
based on heuristic
inferred from DOI database lookup
Towards an automatic method of predicting protein structure by homology: an evaluation of suboptimal sequence alignments
1 reference
stated in
Crossref
reference URL
https://api.crossref.org/works/10.1016%2FS0065-227X%2899%2980007-0
retrieved
7 January 2021
based on heuristic
inferred from DOI database lookup
Knowledge-based prediction of protein structures and the design of novel molecules
1 reference
stated in
Crossref
reference URL
https://api.crossref.org/works/10.1016%2FS0065-227X%2899%2980007-0
retrieved
7 January 2021
based on heuristic
inferred from DOI database lookup
Alignment of the amino acid sequences of distantly related proteins using variable gap penalties
1 reference
stated in
Crossref
reference URL
https://api.crossref.org/works/10.1016%2FS0065-227X%2899%2980007-0
retrieved
7 January 2021
based on heuristic
inferred from DOI database lookup
A variable gap penalty function and feature weights for protein 3-D structure comparisons
1 reference
stated in
Crossref
reference URL
https://api.crossref.org/works/10.1016%2FS0065-227X%2899%2980007-0
retrieved
7 January 2021
based on heuristic
inferred from DOI database lookup
Quantification of secondary structure prediction improvement using multiple alignments.
1 reference
stated in
Crossref
reference URL
https://api.crossref.org/works/10.1016%2FS0065-227X%2899%2980007-0
retrieved
7 January 2021
based on heuristic
inferred from DOI database lookup
Redefining the goals of protein secondary structure prediction
1 reference
stated in
Crossref
reference URL
https://api.crossref.org/works/10.1016%2FS0065-227X%2899%2980007-0
retrieved
7 January 2021
based on heuristic
inferred from DOI database lookup
Prediction of protein secondary structure by combining nearest-neighbor algorithms and multiple sequence alignments
1 reference
stated in
Crossref
reference URL
https://api.crossref.org/works/10.1016%2FS0065-227X%2899%2980007-0
retrieved
7 January 2021
based on heuristic
inferred from DOI database lookup
A simple and fast approach to prediction of protein secondary structure from multiply aligned sequences with accuracy above 70%.
1 reference
stated in
Crossref
reference URL
https://api.crossref.org/works/10.1016%2FS0065-227X%2899%2980007-0
retrieved
7 January 2021
based on heuristic
inferred from DOI database lookup
Using Evolutionary Trees in Protein Secondary Structure Prediction and Other Comparative Sequence Analyses
1 reference
stated in
Crossref
reference URL
https://api.crossref.org/works/10.1016%2FS0065-227X%2899%2980007-0
retrieved
7 January 2021
based on heuristic
inferred from DOI database lookup
Alignment of protein sequences using secondary structure: a modified dynamic programming method
1 reference
stated in
Crossref
reference URL
https://api.crossref.org/works/10.1016%2FS0065-227X%2899%2980007-0
retrieved
7 January 2021
based on heuristic
inferred from DOI database lookup
Mix'n'Match: an improved multiple sequence alignment procedure for distantly related proteins using secondary structure predictions, designed to be independent of the choice of gap penalty and scoring matrix.
1 reference
stated in
Crossref
reference URL
https://api.crossref.org/works/10.1016%2FS0065-227X%2899%2980007-0
retrieved
7 January 2021
based on heuristic
inferred from DOI database lookup
Further developments of protein secondary structure prediction using information theory. New parameters and consideration of residue pairs
1 reference
stated in
Crossref
reference URL
https://api.crossref.org/works/10.1016%2FS0065-227X%2899%2980007-0
retrieved
7 January 2021
based on heuristic
inferred from DOI database lookup
Protein fold recognition by prediction-based threading
1 reference
stated in
Crossref
reference URL
https://api.crossref.org/works/10.1016%2FS0065-227X%2899%2980007-0
retrieved
7 January 2021
based on heuristic
inferred from DOI database lookup
Algorithms for the search of amino acid patterns in nucleic acid sequences
1 reference
stated in
Crossref
reference URL
https://api.crossref.org/works/10.1016%2FS0065-227X%2899%2980007-0
retrieved
7 January 2021
based on heuristic
inferred from DOI database lookup
The protein threading problem with sequence amino acid interaction preferences is NP-complete
1 reference
stated in
Crossref
reference URL
https://api.crossref.org/works/10.1016%2FS0065-227X%2899%2980007-0
retrieved
7 January 2021
based on heuristic
inferred from DOI database lookup
A Method to Identify Protein Sequences That Fold into a Known Three-Dimensional Structure
1 reference
stated in
Crossref
reference URL
https://api.crossref.org/works/10.1016%2FS0065-227X%2899%2980007-0
retrieved
7 January 2021
based on heuristic
inferred from DOI database lookup
Divergent structures of Caenorhabditis elegans cytochrome P450 genes suggest the frequent loss and gain of introns during the evolution of nematodes
1 reference
stated in
Crossref
reference URL
https://api.crossref.org/works/10.1016%2FS0065-227X%2899%2980007-0
retrieved
7 January 2021
based on heuristic
inferred from DOI database lookup
Multiple protein sequence alignment from tertiary structure comparison: assignment of global and residue confidence levels
1 reference
stated in
Crossref
reference URL
https://api.crossref.org/works/10.1016%2FS0065-227X%2899%2980007-0
retrieved
7 January 2021
based on heuristic
inferred from DOI database lookup
Multiple protein structure alignment
1 reference
stated in
Crossref
reference URL
https://api.crossref.org/works/10.1016%2FS0065-227X%2899%2980007-0
retrieved
7 January 2021
based on heuristic
inferred from DOI database lookup
Multiple sequence threading: an analysis of alignment quality and stability.
1 reference
stated in
Crossref
reference URL
https://api.crossref.org/works/10.1016%2FS0065-227X%2899%2980007-0
retrieved
7 January 2021
based on heuristic
inferred from DOI database lookup
Identifiers
DOI
10.1016/S0065-227X(99)80007-0
1 reference
stated in
Europe PubMed Central
PubMed ID
10463075
retrieved
28 July 2017
PubMed ID
10463075
1 reference
stated in
Europe PubMed Central
PubMed ID
10463075
retrieved
28 July 2017
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