Lossless Approximate Pattern Matching: Automated Design of Efficient Search Schemes.

approximate pattern matching integer linear program search schemes sequence alignment

Journal

Journal of computational biology : a journal of computational molecular cell biology
ISSN: 1557-8666
Titre abrégé: J Comput Biol
Pays: United States
ID NLM: 9433358

Informations de publication

Date de publication:
30 Sep 2024
Historique:
medline: 30 9 2024
pubmed: 30 9 2024
entrez: 30 9 2024
Statut: aheadofprint

Résumé

This study introduces a pioneering approach to automate the creation of search schemes for lossless approximate pattern matching. Search schemes are combinatorial structures that define a series of searches over a partitioned pattern. Each search specifies the processing order of these parts and the cumulative lower and upper bounds on the number of errors in each part of the pattern. Together, these searches ensure the identification of all approximate occurrences of a search pattern within a predefined limit of

Identifiants

pubmed: 39344875
doi: 10.1089/cmb.2024.0664
doi:

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Auteurs

Luca Renders (L)

Internet Technology and Data Science Lab, Ghent University, Ghent, Belgium.

Lore Depuydt (L)

Internet Technology and Data Science Lab, Ghent University, Ghent, Belgium.

Sven Rahmann (S)

Center for Bioinformatics Saar, Saarland University, Saarbrücken, Germany.

Jan Fostier (J)

Internet Technology and Data Science Lab, Ghent University, Ghent, Belgium.

Classifications MeSH