Fast profile matching algorithms - A survey

DOI10.1016/J.TCS.2008.01.015MaRDI QIDQ932308zbMATH OpenOpenAlexDBLPWikidataFDO

Authors Cinzia Pizzi, Esko Ukkonen

Publication date 10 July 2008

Published in Theoretical Computer Science (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1016/j.tcs.2008.01.015

zbMATH Keywords

algorithmscomputational complexityposition-specific scoring matrixprofile matchingPSSM

Mathematics Subject Classification ID

Pattern recognition, speech recognition (68T10) Searching and sorting (68P10)

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Cites work

• scientific article; zbMATH DE number 3471577 (Why is no real title available?)
• scientific article; zbMATH DE number 2038766 (Why is no real title available?)
• scientific article; zbMATH DE number 1754502 (Why is no real title available?)
• scientific article; zbMATH DE number 801745 (Why is no real title available?)
• A Space-Economical Suffix Tree Construction Algorithm
• Algorithms on Strings, Trees and Sequences
• Biological Sequence Analysis
• Compression of individual sequences via variable-rate coding
• Efficient string matching
• Large Scale Matching for Position Weight Matrices
• Linear-time construction of suffix arrays (extended abstract)
• On the Power of Profiles for Transcription Factor Binding Site Detection
• On-line construction of suffix trees
• Replacing suffix trees with enhanced suffix arrays
• Some string matching problems from bioinformatics which still need better solutions
• Space efficient linear time construction of suffix arrays

Cited in

(9)

• Motif matching using gapped patterns
• Pattern matching and consensus problems on weighted sequences and profiles
• On-Line Pattern Matching on Uncertain Sequences and Applications
• Streaming \(k\)-mismatch with error correcting and applications
• Calculating PSSM probabilities with lazy dynamic programming
• Fast Matching Method for DNA Sequences
• Large Scale Matching for Position Weight Matrices
• Linear-time computation of prefix table for weighted strings {\&} applications
• scientific article; zbMATH DE number 2087052 (Why is no real title available?)

Describes a project that uses

Uses Software

• PATMAT
• FingerPRINTScan
• MATCH
• JASPAR
• BLAST
• PSI-BLAST
• TRANSFAC

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