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)

zbMATH Keywords

pattern matchingalpha-helix predictionhomology detectionprobabilistic sequence matchingprobabilistic sequence searchingprofile searching

Mathematics Subject Classification ID

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

Recommendations

• Popping superbubbles and discovering clumps: recent developments in biological sequence analysis
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Cites work

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

Cited in

(6)

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

Describes a project that uses

Uses Software

• PROSITE
• ClustalW

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