Application of max-plus algebra to biological sequence comparisons

DOI10.1016/S0304-3975(02)00237-2MaRDI QIDQ1870593zbMATH OpenFDO

Authors Jean-Paul Comet

Publication date 14 May 2003

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

Full work available at URL https://doi.org/10.1016/S0304-3975(02)00237-2

zbMATH Keywords

biological sequence alignmentdynamic programmingmax-plus algebra

Mathematics Subject Classification ID

Formal languages and automata (68Q45) Dynamic programming (90C39)

Recommendations

• The Multiple Sequence Alignment Problem in Biology
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Cites work

• A fast string searching algorithm
• Algorithms for computing finite semigroups
• Boyer-Moore approach to approximate string matching
• Comparison of biosequences
• Dioïds and semirings: Links to fuzzy sets and other applications
• Fast and practical approximate string matching
• Fast Pattern Matching in Strings
• Finding approximate patterns in strings
• scientific article; zbMATH DE number 627763 (Why is no real title available?)
• On the Theory and Computation of Evolutionary Distances
• Performance evaluation of (max,+) automata
• Sequence comparison with concave weighting functions

Cited in

(3)

• Computation of the transient in max-plus linear systems via SMT-solving
• Fast distance multiplication of unit-Monge matrices
• Tropical properties of alignment matrices

Describes a project that uses

Uses Software

• BLAST
• PSI-BLAST
• LASSAP
• Agrep

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