A General Framework for Exact Partially Local Alignments

Falco Kirchner, Nancy Retzlaff, Peter Stadler

Abstract

Multiple sequence alignments are a crucial intermediate step in a plethora of data analysis workflows in computational biology. While multiple sequence alignments are usually constructed with the help of heuristic approximations, exact pairwise alignments are readily computed by dynamic programming algorithms. In the pairwise case, local, global, and semi-global alignments are distinguished, with key applications in pattern discovery, gene comparison, and homology search, respectively. With increasing computing power, exact alignments of triples and even quadruples of sequences have become feasible and recent applications e.g. in the context of breakpoint discovery have shown that mixed local/global multiple alignments can be of practical interest. vaPLA is the first implementation of partially local multiple alignments of a few sequences and provides convenient access to this family of specialized alignment algorithms.

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Paper Citation


in Harvard Style

Kirchner F., Retzlaff N. and Stadler P. (2019). A General Framework for Exact Partially Local Alignments.In Proceedings of the 12th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 3: BIOINFORMATICS, ISBN 978-989-758-353-7, pages 194-200. DOI: 10.5220/0007380001940200


in Bibtex Style

@conference{bioinformatics19,
author={Falco Kirchner and Nancy Retzlaff and Peter Stadler},
title={A General Framework for Exact Partially Local Alignments},
booktitle={Proceedings of the 12th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 3: BIOINFORMATICS,},
year={2019},
pages={194-200},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0007380001940200},
isbn={978-989-758-353-7},
}


in EndNote Style

TY - CONF

JO - Proceedings of the 12th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 3: BIOINFORMATICS,
TI - A General Framework for Exact Partially Local Alignments
SN - 978-989-758-353-7
AU - Kirchner F.
AU - Retzlaff N.
AU - Stadler P.
PY - 2019
SP - 194
EP - 200
DO - 10.5220/0007380001940200