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Finding Similar Regions in Many Sequences

https://doi.org/10.1006/jcss.2002.1823
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/prot.340070105openalex-snapshot
An expectation maximization (EM) algorithm for the identification and characterization of common sites in unaligned biopolymer sequences
inferredcites →https://doi.org/10.1002/prot.340090304openalex-snapshot
A workbench for multiple alignment construction and analysis
inferredcites →https://doi.org/10.1007/3-540-45123-4_10openalex-snapshot
A Polynomial Time Approximation Scheme for the Closest Substring Problem
inferredcites →https://doi.org/10.1007/3-540-58094-8_4openalex-snapshot
Approximation algorithms for multiple sequence alignment
inferredcites →https://doi.org/10.1007/978-1-4684-2001-2openalex-snapshot
Complexity of Computer Computations
inferredcites →https://doi.org/10.1007/978-1-4684-2001-2_9openalex-snapshot
Reducibility among Combinatorial Problems
inferredcites →https://doi.org/10.1007/bf02459500openalex-snapshot
Pattern recognition in several sequences: Consensus and alignment
inferredcites →https://doi.org/10.1007/bf02459504openalex-snapshot
Line geometries for sequence comparisons
inferredcites →https://doi.org/10.1007/bf02460299openalex-snapshot
Efficient methods for multiple sequence alignment with guaranteed error bounds
inferredcites →https://doi.org/10.1016/0014-5793(91)80276-9openalex-snapshot
Methods in enzymology: Volume 183 molecular evolution: Computer analysis of protein and nucleic acid sequences
inferredcites →https://doi.org/10.1016/0076-6879(90)83015-2openalex-snapshot
[13] Consensus patterns in DNA
inferredcites →https://doi.org/10.1017/cbo9780511574931openalex-snapshot
Algorithms on Strings, Trees and Sequences
inferredcites →https://doi.org/10.1017/cbo9780511814075openalex-snapshot
Randomized Algorithms
inferredcites →https://doi.org/10.1073/pnas.86.4.1183openalex-snapshot
Identifying protein-binding sites from unaligned DNA fragments.
inferredcites →https://doi.org/10.1073/pnas.88.13.5699openalex-snapshot
Specificity of the Mnt protein determined by binding to randomized operators.
inferredcites →https://doi.org/10.1089/cmb.1994.1.337openalex-snapshot
On the Complexity of Multiple Sequence Alignment
inferredcites →https://doi.org/10.1093/bioinformatics/11.4.379openalex-snapshot
Identification of common motifs in unaligned DNA sequences: application to Escherichia coli Lrp regulon
inferredcites →https://doi.org/10.1093/bioinformatics/11.5.477openalex-snapshot
Eukaryotic promoter recognition by binding sites for transcription factors
inferredcites →https://doi.org/10.1093/bioinformatics/11.5.563openalex-snapshot
MATRIX SEARCH 1.0: a computer program that scans DNA sequences for transcriptional elements using a database of weight matrices
inferredcites →https://doi.org/10.1093/bioinformatics/12.2.157openalex-snapshot
SIGNAL SCAN 4.0: additional databases and sequence formats
inferredcites →https://doi.org/10.1093/bioinformatics/8.1.57openalex-snapshot
A search for common patterns in many sequences
inferredcites →https://doi.org/10.1093/nar/14.22.9095openalex-snapshot
Multiple sequence alignment by consensus
inferredcites →https://doi.org/10.1093/nar/17.7.2421openalex-snapshot
Predictive motifs derived from cytosine methyltransferases
inferredcites →https://doi.org/10.1137/0152101openalex-snapshot
Multiple Alignment, Communication Cost, and Graph Matching
inferredcites →https://doi.org/10.1145/506147.506150openalex-snapshot
On the closest string and substring problems

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Sharper Upper and Lower Bounds for an Approximation Scheme for Consensus-Pattern
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An Upper Bound on the Hardness of Exact Matrix Based Motif Discovery
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On the Longest Common Rigid Subsequence Problem
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New Bounds for Motif Finding in Strong Instances
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A Compact Mathematical Programming Formulation for DNA Motif Finding
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Mining Spatial Association Rules for Composite Motif Discovery
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Closest String and Substring Problems
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Algorithms for Closest and Farthest String Problems via Rank Distance
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Trajectory Comparison in a Vehicular Network I: Computing a Consensus Trajectory
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On the Kernelization Complexity of String Problems
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State-of-the-Art Approaches for String and Text Analysis
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Grundlagen der Molekularbiologie
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Bestimmung von Signalen in DNA-Sequenzen
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Settling the Intractability of Multiple Alignment
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Randomized Algorithms for Motif Detection
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On Exact and Approximation Algorithms for Distinguishing Substring Selection
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Finding Signals in DNA Sequences
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Identification of Distinguishing Motifs
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Segmentation and Annotation of Audiovisual Recordings Based on Automated Speech Recognition
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On the Structure of Small Motif Recognition Instances
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Detecting Motifs in a Large Data Set: Applying Probabilistic Insights to Motif Finding
inferred← citeshttps://doi.org/10.1007/978-3-642-02270-8_27openalex-snapshot
Efficient Algorithms for the Closest String and Distinguishing String Selection Problems
inferred← citeshttps://doi.org/10.1007/978-3-642-03784-9_24openalex-snapshot
Faster Algorithms for Sampling and Counting Biological Sequences
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Why Large Closest String Instances Are Easy to Solve in Practice
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On the Hardness of Counting and Sampling Center Strings
inferred← citeshttps://doi.org/10.1007/978-3-642-22993-0_17openalex-snapshot
The Bounded Search Tree Algorithm for the Closest String Problem Has Quadratic Smoothed Complexity
inferred← citeshttps://doi.org/10.1007/978-3-642-27848-8_73-2openalex-snapshot
Closest String and Substring Problems
inferred← citeshttps://doi.org/10.1007/978-3-642-29038-1_34openalex-snapshot
Efficient Algorithm for Mining Correlated Protein-DNA Binding Cores
inferred← citeshttps://doi.org/10.1007/978-3-642-30191-9_1openalex-snapshot
Trie-based Apriori Motif Discovery Approach
inferred← citeshttps://doi.org/10.1007/978-3-642-31265-6_33openalex-snapshot
On the Closest String via Rank Distance
inferred← citeshttps://doi.org/10.1007/978-3-642-31265-6_34openalex-snapshot
On Approximating String Selection Problems with Outliers
inferred← citeshttps://doi.org/10.1007/978-3-662-48350-3_21openalex-snapshot
Consensus Patterns (Probably) Has no EPTAS
inferred← citeshttps://doi.org/10.1007/s00224-004-1185-zopenalex-snapshot
Parameterized Intractability of Distinguishing Substring Selection
inferred← citeshttps://doi.org/10.1007/s00453-008-9175-1openalex-snapshot
On the Longest Common Rigid Subsequence Problem
inferred← citeshttps://doi.org/10.1007/s00453-019-00647-9openalex-snapshot
Consensus Strings with Small Maximum Distance and Small Distance Sum
inferred← citeshttps://doi.org/10.1007/s00493-006-0011-4openalex-snapshot
On The Parameterized Intractability Of Motif Search Problems*
inferred← citeshttps://doi.org/10.1007/s10710-014-9232-2openalex-snapshot
Multiobjective optimization algorithms for motif discovery in DNA sequences
inferred← citeshttps://doi.org/10.1007/s10878-009-9277-yopenalex-snapshot
Anonymizing binary and small tables is hard to approximate
inferred← citeshttps://doi.org/10.1007/s10878-022-00909-3openalex-snapshot
Computing a consensus trajectory in a vehicular network
inferred← citeshttps://doi.org/10.1007/s11227-014-1266-yopenalex-snapshot
Parallelizing and optimizing a hybrid differential evolution with Pareto tournaments for discovering motifs in DNA sequences
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A hybrid MPI/OpenMP parallel implementation of NSGA-II for finding patterns in protein sequences
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On the approximability of the Maximum Agreement SubTree and Maximum Compatible Tree problems
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A comprehensive survey on genetic algorithms for DNA motif prediction
inferred← citeshttps://doi.org/10.1016/j.jda.2004.08.015openalex-snapshot
Hardness results for the center and median string problems under the weighted and unweighted edit distances
inferred← citeshttps://doi.org/10.1016/j.jda.2006.10.006openalex-snapshot
An upper bound on the hardness of exact matrix based motif discovery
inferred← citeshttps://doi.org/10.1016/j.jda.2009.12.001openalex-snapshot
On the complexity of finding gapped motifs
inferred← citeshttps://doi.org/10.1016/j.jda.2011.04.001openalex-snapshot
A cost-aggregating integer linear program for motif finding
inferred← citeshttps://doi.org/10.1016/j.jtbi.2010.02.010openalex-snapshot
Motif discovery using an immune genetic algorithm
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Parallel implementation of quorum planted (ℓ, d ) motif search on multi-core/many-core platforms
inferred← citeshttps://doi.org/10.1016/j.parco.2018.04.001openalex-snapshot
Searching for common patterns on protein sequences by means of a parallel hybrid honey-bee mating optimization algorithm
inferred← citeshttps://doi.org/10.1016/j.tcs.2013.05.037openalex-snapshot
On approximating string selection problems with outliers
inferred← citeshttps://doi.org/10.1016/j.tcs.2018.03.024openalex-snapshot
On the kernelization complexity of string problems
inferred← citeshttps://doi.org/10.1016/j.tcs.2022.12.033openalex-snapshot
Hardness and approximation of multiple sequence alignment with column score
inferred← citeshttps://doi.org/10.1089/cmb.2006.13.1323openalex-snapshot
Settling the Intractability of Multiple Alignment
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780198566076.001.0001openalex-snapshot
Invitation to Fixed-Parameter Algorithms
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780198566076.002.0004openalex-snapshot
Copyright Page
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780198566076.002.0005openalex-snapshot
PREFACE
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780198566076.003.0001openalex-snapshot
INTRODUCTION TO FIXED-PARAMETER ALGORITHMS
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780198566076.003.0002openalex-snapshot
PRELIMINARIES AND AGREEMENTS
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780198566076.003.0003openalex-snapshot
PARAMETERIZED COMPLEXITY THEORY—A PRIMER
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780198566076.003.0004openalex-snapshot
VERTEX COVER—AN ILLUSTRATIVE EXAMPLE
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780198566076.003.0005openalex-snapshot
THE ART OF PROBLEM PARAMETERIZATION
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780198566076.003.0006openalex-snapshot
SUMMARY AND CONCLUDING REMARKS
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780198566076.003.0007openalex-snapshot
DATA REDUCTION AND PROBLEM KERNELS
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780198566076.003.0008openalex-snapshot
DEPTH-BOUNDED SEARCH TREES
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780198566076.003.0009openalex-snapshot
DYNAMIC PROGRAMMING
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780198566076.003.0010openalex-snapshot
TREE DECOMPOSITIONS OF GRAPHS
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780198566076.003.0011openalex-snapshot
FURTHER ADVANCED TECHNIQUES
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780198566076.003.0012openalex-snapshot
SUMMARY AND CONCLUDING REMARKS
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780198566076.003.0013openalex-snapshot
PARAMETERIZED COMPLEXITY THEORY
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780198566076.003.0014openalex-snapshot
CONNECTIONS TO APPROXIMATION ALGORITHMS
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780198566076.003.0015openalex-snapshot
SELECTED CASE STUDIES
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780198566076.003.0016openalex-snapshot
ZUKUNFTSMUSIK
inferred← citeshttps://doi.org/10.1093/bioinformatics/btl371openalex-snapshot
Finding motifs from all sequences with and without binding sites
inferred← citeshttps://doi.org/10.1093/bioinformatics/btm606openalex-snapshot
TFBS identification based on genetic algorithm with combined representations and adaptive post-processing
inferred← citeshttps://doi.org/10.1093/bioinformatics/btq682openalex-snapshot
Discovering approximate-associated sequence patterns for protein–DNA interactions
inferred← citeshttps://doi.org/10.1093/comjnl/bxv055openalex-snapshot
A Comparative Study of Different Motif Occurrence Models Applied to a Hybrid Multiobjective Shuffle Frog Leaping Algorithm
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FisherMP: fully parallel algorithm for detecting combinatorial motifs from large ChIP-seq datasets
inferred← citeshttps://doi.org/10.1093/nar/gks749openalex-snapshot
Subtypes of associated protein–DNA (Transcription Factor-Transcription Factor Binding Site) patterns
inferred← citeshttps://doi.org/10.1109/bibe.2005.12openalex-snapshot
An Efficient Algorithm for the Extended (l, d)-Motif Problem with Unknown Number of Binding Sites
inferred← citeshttps://doi.org/10.1109/bibe.2006.253318openalex-snapshot
Discovering DNA Motifs with Nucleotide Dependency
inferred← citeshttps://doi.org/10.1109/bibm.2012.6392682openalex-snapshot
Identifying protein binding functionality of protein family sequences by Aligned Pattern clusters
inferred← citeshttps://doi.org/10.1109/bibmw.2011.6112372openalex-snapshot
Synthesizing Aligned Random Pattern Digraphs from protein sequence patterns
inferred← citeshttps://doi.org/10.1109/bibmw.2012.6470286openalex-snapshot
Identifying protein binding functionality of protein family sequences by aligned pattern clusters
inferred← citeshttps://doi.org/10.1109/cec.2008.4631120openalex-snapshot
An Estimation of Distribution Algorithm for Motif Discovery
inferred← citeshttps://doi.org/10.1109/cec.2010.5585924openalex-snapshot
Generic spaced DNA motif discovery using Genetic Algorithm
inferred← citeshttps://doi.org/10.1109/cibcb.2013.6595409openalex-snapshot
Genetic algorithm for dimer-led and error-restricted spaced motif discovery
inferred← citeshttps://doi.org/10.1109/dexa.2014.24openalex-snapshot
A Consensus Algorithm for Simple Motifs Finding
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Finding Transcription Factor Binding Sites with Indels
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Predicting Approximate Protein-DNA Binding Cores Using Association Rule Mining
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ListMotif: A time and memory efficient algorithm for weak motif discovery
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The Closest Substring problem with small distances
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A Genetic Approximation of Closest String via Rank Distance
inferred← citeshttps://doi.org/10.1109/tcbb.2007.70220openalex-snapshot
DNA Motif Representation with Nucleotide Dependency
inferred← citeshttps://doi.org/10.1109/tcbb.2009.25openalex-snapshot
A Cluster Refinement Algorithm for Motif Discovery
inferred← citeshttps://doi.org/10.1109/tcbb.2011.21openalex-snapshot
Fast Exact Algorithms for the Closest String and Substring Problems with Application to the Planted (L,d)-Motif Model
inferred← citeshttps://doi.org/10.1109/tcbb.2012.84openalex-snapshot
On the Hardness of Counting and Sampling Center Strings
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Modeling Associated Protein-DNA Pattern Discovery with Unified Scores
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Memetic Algorithms for De Novo Motif Discovery
inferred← citeshttps://doi.org/10.1137/060673898openalex-snapshot
Closest Substring Problems with Small Distances
inferred← citeshttps://doi.org/10.1137/19m1255781openalex-snapshot
Tight Hardness Results for Consensus Problems on Circular Strings and Time Series
inferred← citeshttps://doi.org/10.1142/9781848162648_0004openalex-snapshot
VOTING ALGORITHMS FOR THE MOTIF FINDING PROBLEM
inferred← citeshttps://doi.org/10.1142/s0219720005001508openalex-snapshot
RANDOMIZED ALGORITHMS FOR MOTIF DETECTION
inferred← citeshttps://doi.org/10.1142/s0219720006001692openalex-snapshot
ALGORITHMS FOR CHALLENGING MOTIF PROBLEMS
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Challenges rising from learning motif evaluation functions using genetic programming
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Some open problems in computational molecular biology
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On the closest string and substring problems
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Discovering multiple realistic TFBS motifs based on a generalized model
inferred← citeshttps://doi.org/10.1186/1471-2105-11-s1-s11openalex-snapshot
Fast motif recognition via application of statistical thresholds
inferred← citeshttps://doi.org/10.1186/1471-2105-11-s11-s8openalex-snapshot
RecMotif: a novel fast algorithm for weak motif discovery
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Closest string with outliers
inferred← citeshttps://doi.org/10.1186/1477-5956-11-s1-s8openalex-snapshot
Ranking and compacting binding segments of protein families using aligned pattern clusters
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Multiple Sequence Alignment as a Facility-Location Problem
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An Efficient Rank Based Approach for Closest String and Closest Substring
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An efficient motif discovery algorithm with unknown motif length and number of binding sites
inferred← citeshttps://doi.org/10.1504/ijdmb.2015.070833openalex-snapshot
TrieAMD: a scalable and efficient apriori motif discovery approach
inferred← citeshttps://doi.org/10.20381/ruor-5077openalex-snapshot
MotifGP: DNA Motif Discovery Using Multiobjective Evolution
inferred← citeshttps://doi.org/10.2197/ipsjdc.3.174openalex-snapshot
Hardness Results on Local Multiple Alignment of Biological Sequences
inferred← citeshttps://doi.org/10.32657/10356/64820openalex-snapshot
Effective graph-based algorithms for weak motif discovery in genomic sequences
inferred← citeshttps://doi.org/10.3934/mbe.2019075openalex-snapshot
A multi-objective imperialist competitive algorithm (MOICA) for finding motifs in DNA sequences
inferred← citeshttps://doi.org/10.4018/978-1-4666-1785-8.ch001openalex-snapshot
Identification of Distinguishing Motifs
inferred← citeshttps://doi.org/10.4018/jkdb.2010070104openalex-snapshot
Identification of Distinguishing Motifs
inferred← citeshttps://doi.org/10.4230/lipics.cpm.2020.11openalex-snapshot
Summarizing Diverging String Sequences, with Applications to Chain-Letter Petitions
inferred← citeshttps://doi.org/10.4230/lipics.esa.2018.34openalex-snapshot
A QPTAS for Gapless MEC
inferred← citeshttps://doi.org/10.4230/lipics.mfcs.2021.48openalex-snapshot
Matching Patterns with Variables Under Hamming Distance
inferred← citeshttps://doi.org/10.48550/arxiv.1111.0376openalex-snapshot
Outlier Detection for DNA Fragment Assembly
inferred← citeshttps://doi.org/10.48550/arxiv.cs/0205056openalex-snapshot
Parameterized Intractability of Motif Search Problems
inferred← citeshttps://doi.org/10.53846/goediss-10344openalex-snapshot
Matching Patterns with Variables in Approximate Settings
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