Fast profile matching algorithms - A survey

DOI10.1016/J.TCS.2008.01.015zbMath1140.68475DBLPjournals/tcs/PizziU08OpenAlexW2105318270WikidataQ58054166 ScholiaQ58054166MaRDI QIDQ932308

Esko Ukkonen, Cinzia Pizzi

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

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

Related Items (5)

Motif matching using gapped patterns ⋮ On-Line Pattern Matching on Uncertain Sequences and Applications ⋮ Linear-time computation of prefix table for weighted strings {\&} applications ⋮ Pattern matching and consensus problems on weighted sequences and profiles ⋮ Streaming \(k\)-mismatch with error correcting and applications

Uses Software

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

Cites Work

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• Some string matching problems from bioinformatics which still need better solutions
• Replacing suffix trees with enhanced suffix arrays
• On-line construction of suffix trees
• Linear-Time Construction of Suffix Arrays
• Space Efficient Linear Time Construction of Suffix Arrays
• Efficient string matching
• A Space-Economical Suffix Tree Construction Algorithm
• Compression of individual sequences via variable-rate coding
• Biological Sequence Analysis
• Algorithms on Strings, Trees and Sequences
• On the Power of Profiles for Transcription Factor Binding Site Detection
• Large Scale Matching for Position Weight Matrices

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