ArticleAlgorithms for molecular biology : AMB2019
Kohdista: an efficient method to index and query possible Rmap alignments.
Article in Algorithms for molecular biology : AMB, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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4 citing papers in PubMed.
- Formal verification of bioinformatics software using model checking and theorem proving.Briefings in bioinformatics · 2025Article
- Fast and efficient Rmap assembly using the Bi-labelled de Bruijn graph.Algorithms for molecular biology : AMB · 2021Article
- FaNDOM: Fast nested distance-based seeding of optical maps.Patterns (New York, N.Y.) · 2021Article
- Advances in optical mapping for genomic research.Computational and structural biotechnology journal · 2020Review
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3 authors.
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Abstract
backgroundGenome-wide optical maps are ordered high-resolution restriction maps that give the position of occurrence of restriction cut sites corresponding to one or more restriction enzymes. These genome-wide optical maps are assembled using an overlap-layout-consensus approach using raw optical map data, which are referred to as Rmaps. Due to the high error-rate of Rmap data, finding the overlap between Rmaps remains challenging.
resultsWe present Kohdista, which is an index-based algorithm for finding pairwise alignments between single molecule maps (
conclusionwe demonstrate Kohdista is the only method that is capable of finding a significant number of high quality pairwise Rmap alignments for large eukaryote organisms in reasonable time.
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