Extended pairwise local alignment of wild card DNA/RNA sequences using dynamic programming

DOI10.1080/00949655.2014.928294MaRDI QIDQ5220696zbMATH OpenOpenAlexFDO

Authors Axel Fürstberger, Markus Maucher, Hans A. Kestler

Publication date 27 March 2020

Published in Journal of Statistical Computation and Simulation (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1080/00949655.2014.928294

zbMATH Keywords

dynamic programmingnucleotide sequenceslocal alignmentprotein sequencesDNA/RNA sequencesbest-/worst-case analysiswild bases alignment

Mathematics Subject Classification ID

Applications of statistics to biology and medical sciences; meta analysis (62P10) Learning and adaptive systems in artificial intelligence (68T05) Protein sequences, DNA sequences (92D20) Software, source code, etc. for problems pertaining to biology (92-04)

Recommendations

• Pairwise sequence alignment revisited -- genetic algorithms and cosine functions
• A local algorithm for DNA sequence alignment with inversions
• The Multiple Sequence Alignment Problem in Biology
• Partially local multi-way alignments
• Parametric optimization of sequence alignment

Cites work

• Fast string kernels using inexact matching for protein sequences

Cited in

(2)

• Proceedings of Reisensburg 2013
• Local Alignment of RNA Sequences with Arbitrary Scoring Schemes

Describes a project that uses

Uses Software

• GitHub
• G-BLASTN
• Amazon EC2
• ESyPred3D
• FASTA3
• T-coffee

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