Multiple DNA and protein sequence alignment based on segment-to-segment comparison.

DOI10.1073/PNAS.93.22.12098MaRDI QIDQ5690790zbMATH OpenOpenAlexWikidataFDO

Authors B. Morgenstern, Andreas W. M. Dress, Thomas Werner

Publication date 4 June 1997

Published in Proceedings of the National Academy of Sciences (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1073/pnas.93.22.12098

zbMATH Keywords

alignment algorithmconsistent equivalence relationsDNA sequencesdynamic programmingfragment comparisonfunctional-site identificationmultiple alignmentspartial alignmentsprotein sequencesribonucleasesegment-to-segment comparisonsequence similarity

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Protein sequences, DNA sequences (92D20)

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Cited in

(23)

• Aligning DNA sequences to minimize the change in protein
• A polyhedral approach to sequence alignment problems
• A scheme for multiple sequence alignment optimization -- an improvement based on family representative mechanics features
• New method for global alignment of 2 DNA sequences by the tree data structure
• The number of standard and of effective multiple alignments
• A simple and space-efficient fragment-chaining algorithm for alignment of DNA and protein sequences
• A non-local gap-penalty for profile alignment
• Compositional properties of alignments
• Magnus representation of genome sequences
• Pattern-constrained multiple polypeptide sequence alignment
• Extracting approximate patterns
• Pairwise sequence alignment revisited -- genetic algorithms and cosine functions
• Multiple sequence alignment using external sources of information
• A NEW MIDDLE PATH APPROACH FOR ALIGNMENTS IN BLAST
• Protein sequence alignment taking the structure of peptide bond
• A protein coding gene alignment algorithm based on SPA
• Multiple protein sequence alignment using double-dynamic programming
• Phase-only filtering for the masses (of DNA Data): a new approach to sequence alignment
• Multiple alignment of biological sequences with gap flexibility
• A path selection approach to global pairwise sequence alignment using integer linear optimization†
• Global pairwise sequence alignment through mixed-integer linear programming: a template-free approach
• Fast multiple alignment of ungapped DNA sequences using information theory and a relaxation method
• Four billion years: the story of an ancient protein family

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