Fast profile matching algorithms - A survey

DOI10.1016/j.tcs.2008.01.015zbMath1140.68475WikidataQ58054166 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

algorithms; computational complexity; position-specific scoring matrix; profile matching; PSSM

Mathematics Subject Classification ID

68P10: Searching and sorting

68T10: Pattern recognition, speech recognition

Related Items

Motif matching using gapped patterns, 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, On-Line Pattern Matching on Uncertain Sequences and Applications

Uses Software

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

Cites Work

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• Algorithms on Strings, Trees and Sequences
• On the Power of Profiles for Transcription Factor Binding Site Detection
• Large Scale Matching for Position Weight Matrices