Some string matching problems from bioinformatics which still need better solutions

DOI10.1016/S1570-8667(03)00062-5MaRDI QIDQ876702zbMATH OpenFDO

Authors Gaston H. Gonnet

Publication date 26 April 2007

Published in Journal of Discrete Algorithms (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1016/S1570-8667(03)00062-5

zbMATH Keywords

alpha-helix predictionhomology detectionpattern matchingprobabilistic sequence matchingprobabilistic sequence searchingprofile searching

Mathematics Subject Classification ID

Nonnumerical algorithms (68W05) Computational methods for problems pertaining to biology (92-08) Biochemistry, molecular biology (92C40)

Recommendations

• Popping superbubbles and discovering clumps: recent developments in biological sequence analysis
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• scientific article; zbMATH DE number 828444
• A new approach to pattern matching in degenerate DNA/RNA sequences and distributed pattern matching
• Efficient algorithms for similarity search

Cites work

• A fast string searching algorithm
• Fast Pattern Matching in Strings
• scientific article; zbMATH DE number 140461 (Why is no real title available?)
• Probabilistic ancestral sequences and multiple alignments

Cited in

(6)

• Identifying periodic occurrences of a template with applications to protein structure
• Towards efficient searching on the secondary structure of protein sequences
• Preface: Foundations of bioinformatics.
• String Matching for the Novice
• Efficient algorithms for similarity search
• Fast profile matching algorithms - A survey

Describes a project that uses

Uses Software

• ClustalW
• PROSITE

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