Online citations, reference lists, and bibliographies.
← Back to Search

Some Biological Sequence Metrics

M. Waterman, T. Smith, W. Beyer
Published 1976 · Mathematics

Cite This
Download PDF
Analyze on Scholarcy
Share
Abstract Some new metrics are introduced to measure the distance between biological sequences, such as amino acid sequences or nucleotide sequences. These metrics generalize a metric of Sellers, who considered only single deletions, mutations, and insertions. The present metrics allow, for example, multiple deletions and insertions and single mutations. They also allow computation of the distance among more than two sequences. Algorithms for computing the values of the metrics are given which also compute best alignments. The connection with the information theory approach of Reichert, Cohen, and Wong is discussed.
This paper references
10.1016/0025-5564(75)90064-4
Matching code sequences utilizing context free quality measures
D. N. Cohen (1975)
Locating gaps in amino acid sequences to optimize the homology EUY 1-11. between two proteins
W M Fitch (1969)
10.1016/0022-2836(73)90369-0
A test for nucleotide sequence homology.
D. Sankoff (1973)
10.1002/FOOD.19710150234
Margaret O. Dayhoff: Atlas of Protein Sequence and Structure 1969 (Volume 4) XXIV u. 361 S., 21 Ausklapptafeln, 68 Abb. und zahlreiche Tabellen. National Biomedical Research Foundation, Silver Spring/Maryland 1969. Preis $ 12,50
P. Meisel (1971)
10.1016/0022-2836(70)90089-6
An evaluation of the relatedness of proteins based on comparison of amino acid sequences.
J. Haber (1970)
10.1016/0010-4825(74)90006-7
A generalized method for matching informational macromolecular code sequences.
A. Wong (1974)
Mathematical Taxonomy
N Jardine (1971)
10.1016/0025-5564(74)90028-5
A molecular sequence metric and evolutionary trees
W. Beyer (1974)
Locating gaps in amino acid sequences to optimize the homology EUY
A. J. GIBES AND G. A. MCINTYRE (1970)
METRICS IN BIOLOGY, AN INTRODUCTION.
W. Beyer (1972)
A General Method Applicable to the Search for Similarities in the Amino Acid Sequence of Two Proteins
CHRISTUS
10.1016/0022-2836(70)90057-4
A general method applicable to the search for similarities in the amino acid sequence of two proteins.
S. B. Needleman (1970)
Atlas of protein sequence and structure
M. A. Chang (1965)
10.1016/0022-5193(73)90088-X
An application of information theory to genetic mutations and the matching of polypeptide sequences.
T. Reichert (1973)
KOSHLAND, An evaluation of the relatedness of proteins based on comparison of amino acid sequences
D.E.J.E. HABER (1970)
10.1111/J.1432-1033.1970.TB01046.X
The Diagram, a Method for Comparing Sequences
A. Gibbs (1970)
10.1146/ANNUREV.BB.01.060172.001425
Some ideas and prospects in biomathematics.
S. Ulam (1972)
10.1137/0126070
On the Theory and Computation of Evolutionary Distances
P. Sellers (1974)
10.1016/S0022-2836(66)80258-9
An improved method of testing for evolutionary homology.
Walter M. Fitch (1966)
10.1073/PNAS.69.1.4
Matching sequences under deletion-insertion constraints.
D. Sankoff (1972)



This paper is referenced by
10.12928/TELKOMNIKA.V13I2.1415
Comparison of Data Partitioning Schema of Parallel Pairwise Alignment on Shared Memory System
A. Akbar (2015)
10.12785/AMIS/071L29
Isomorphism Distance in Multidimensional Time Series and Similarity Search
Guo Wen-sheng (2013)
Quantifying Local Reliability of Sequence Alignments Using Mean Field Annealing
C. Peterson ()
10.1016/j.tcs.2008.01.008
Computing similarity of run-length encoded strings with affine gap penalty
J. Kim (2008)
Unsupervised Duplicate Detection
Andrzej Bieszczad Date (2012)
10.1016/0020-0255(92)90065-G
Amino acid sequences and DP matching: A new method for alignment
M. Ohya (1992)
10.1007/978-3-642-36257-6_11
A Practical Guide to Entity Resolution with OYSTER
John R. Talburt (2013)
10.1007/978-1-4419-5906-5_1281
Record Linkage
Stasha Ann Bown Larsen (2011)
10.1145/146637.146656
Sparse dynamic programming II: convex and concave cost functions
D. Eppstein (1992)
10.1006/JMBI.1996.0679
Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed by reference to structural alignments.
O. Gotoh (1996)
10.1117/12.304857
Multiple protein sequence comparison by genetic algorithms
R. R. Gonzalez (1998)
A bioinformaticians view on the evolution of smell perception
Patrizia Anders (2006)
10.1214/08-AOS663
ESTIMATING THE GUMBEL SCALE PARAMETER FOR LOCAL ALIGNMENT OF RANDOM SEQUENCES BY IMPORTANCE SAMPLING WITH STOPPING TIMES.
Yonil Park (2009)
10.1109/FPT.2006.270350
Hardalign: a parallel pairwise alignment hardware application
G. L. Moritz (2006)
Duplicate Detection in Probabilistic Relational Databases
Fabian Panse (2015)
T-cell receptor repertoire sequencing in health and disease
J. Heather (2015)
Efficient algorithms for sequence analysis with concave and convex gap costs
D. Eppstein (1989)
Errata for “ A Metric Model of Amino Acid Substitution ”
Weijia Xu (2005)
10.1101/103101
A Parallel Multiobjective Metaheuristic for Multiple Sequence Alignment
A. Rubio-Largo (2017)
Local Aligner for Massive Biological Data
Hannes Hauswedell (2013)
10.1016/0378-1119(96)00123-0
A general method for fast multiple sequence alignment.
U. Tönges (1996)
10.14778/1920841.1920915
Exploiting content redundancy for web information extraction
P. Gulhane (2010)
10.1016/J.JMAA.2010.05.001
The mean value of the squared path-difference distance for rooted phylogenetic trees
A. Mir (2009)
Supertree Construction: Opportunities and Challenges
T. Warnow (2018)
A Novel Approach for Handling Unknown Word Problem in Chinese-Vietnamese Machine Translation
P. Tran (2014)
Lecture 2 : Sequence Comparison-August 20 , 2004
Vikram Mallur ()
Unsupervised Duplicate Detection ( UDD ) Of Query Results from Multiple Web Databases
Andrzej Bieszczad Date (2011)
Systematics: A Course of Lectures
W. Wheeler (2012)
10.1038/326347A0
Knowledge-based prediction of protein structures and the design of novel molecules
T. Blundell (1987)
10.1007/s11600-019-00381-4
Data integration for earthquake disaster using real-world data
Chuanzhao Tian (2019)
10.1561/1900000045
Trends in Cleaning Relational Data: Consistency and Deduplication
Ihab F. Ilyas (2015)
A Survey: Detection of Duplicate Record
Dewendra Bharambe (2012)
See more
Semantic Scholar Logo Some data provided by SemanticScholar