Compositional properties of alignments

DOI10.1007/S11786-020-00496-8MaRDI QIDQ2071523zbMATH OpenOpenAlexFDO

Authors Sarah J. Berkemer, Christian Höner zu Siederdissen, Peter F. Stadler

Publication date 28 January 2022

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

Copyright license Creative Commons Attribution 4.0 International

Full work available at URL https://doi.org/10.1007/s11786-020-00496-8

zbMATH Keywords

projectionpartial ordersubgraph isomorphismmultiple sequence alignmenttree alignment

Mathematics Subject Classification ID

Computer science (68-XX)

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• Monge properties of sequence alignment
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Cites work

• scientific article; zbMATH DE number 1543363 (Why is no real title available?)
• Algebraic dynamic programming on trees
• Alignment of trees -- an alternative to tree edit
• Biological Sequence Analysis
• Comparing Top k Lists
• Comparison of biosequences
• Exact algorithm for the maximum induced planar subgraph problem
• Fifty years of graph matching, network alignment and network comparison
• Fixed Parameter Tractable Alignment of RNA Structures Including Arbitrary Pseudoknots
• Multiple DNA and protein sequence alignment based on segment-to-segment comparison.
• Non-approximability of weighted multiple sequence alignment.
• Partially local multi-way alignments
• Phylogenetic footprinting and consistent sets of local aligments
• Sneaking around concatmap, efficient combinators for dynamic programming
• Subgraph isomorphism, matching relational structures and maximal cliques
• The Multiple Sequence Alignment Problem in Biology
• The complexity of multiple sequence alignment with SP-score that is a metric

Cited in

(3)

• scientific article; zbMATH DE number 6395612 (Why is no real title available?)
• Hardness and approximation of multiple sequence alignment with column score
• Relational Sequence Alignments and Logos

Describes a project that uses

Uses Software

• BLAST
• PSI-BLAST
• Clustal X
• tracker2
• T-coffee
• MUSCLE
• DIALIGN
• ProbCons
• MAFFT

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