A simple and space-efficient fragment-chaining algorithm for alignment of DNA and protein sequences

DOI10.1016/S0893-9659(01)00085-4zbMath1015.92013WikidataQ127740538 ScholiaQ127740538MaRDI QIDQ1861731

B. Morgenstern

Publication date: 10 March 2003

Published in: Applied Mathematics Letters (Search for Journal in Brave)

zbMATH Keywords

complexitydynamic programmingsequence alignmentstring algorithmfragment chaining

Mathematics Subject Classification ID

Dynamic programming (90C39) Biochemistry, molecular biology (92C40) Complexity and performance of numerical algorithms (65Y20) Computational methods for problems pertaining to biology (92-08)

Related Items (5)

Fuzzy polynucleotide spaces and metrics ⋮ Co-linear chaining with overlaps and gap costs ⋮ An extension of fuzzy topological approach for comparison of genetic sequences ⋮ A metric space to study differences between polynucleotides ⋮ A study of entropy/clarity of genetic sequences using metric spaces and fuzzy sets

Uses Software

• Balibase
• DIALIGN
• GABIOS-LIB

Cites Work

• Unnamed Item
• A polyhedral approach to sequence alignment problems
• Linear-space algorithms that build local alignments from fragments
• A linear space algorithm for computing maximal common subsequences
• Sparse dynamic programming I
• Multiple DNA and protein sequence alignment based on segment-to-segment comparison.

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