ArticleBioinformatics (Oxford, England)2016
Maligner: a fast ordered restriction map aligner.
Article in Bioinformatics (Oxford, England), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- DOM: Dual Optical Mapping Integrating Sequence-Specific Barcodes and A/T Density Profiles.Small methods · 2026Article
- Article
- DOGMA: de novo assembly of densely labelled optical DNA maps using a matrix profile approach.PloS one · 2025Article
- Canonical terpene synthases in arthropods: Intraphylum gene transfer.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- High contiguity de novo genome assembly and DNA modification analyses for the fungus fly, Sciara coprophila, using single-molecule sequencing.BMC genomics · 2021Article
- 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
- Optical map guided genome assembly.BMC bioinformatics · 2020Article
- Identifying microbial species by single-molecule DNA optical mapping and resampling statistics.NAR genomics and bioinformatics · 2020Article
- Fast and accurate correction of optical mapping data via spaced seeds.Bioinformatics (Oxford, England) · 2020Article
- Advances in optical mapping for genomic research.Computational and structural biotechnology journal · 2020Review
- OMMA enables population-scale analysis of complex genomic features and phylogenomic relationships from nanochannel-based optical maps.GigaScience · 2019Article
- Modern technologies and algorithms for scaffolding assembled genomes.PLoS computational biology · 2019Review
- Kohdista: an efficient method to index and query possible Rmap alignments.Algorithms for molecular biology : AMB · 2019Article
- Error correcting optical mapping data.GigaScience · 2018Article
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3 authors.
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Abstract
motivationThe Optical Mapping System discovers structural variants and potentiates sequence assembly of genomes via scaffolding and comparisons that globally validate or correct sequence assemblies. Despite its utility, there are few publicly available tools for aligning optical mapping datasets.
resultsHere we present software, named 'Maligner', for the alignment of both single molecule restriction maps (Rmaps) and in silico restriction maps of sequence contigs to a reference. Maligner provides two modes of alignment: an efficient, sensitive dynamic programming implementation that scales to large eukaryotic genomes, and a faster indexed based implementation for finding alignments with unmatched sites in the reference but not the query. We compare our software to other publicly available tools on Rmap datasets and show that Maligner finds more correct alignments in comparable runtime. Lastly, we introduce the M-Score statistic for normalizing alignment scores across restriction maps and demonstrate its utility for selecting high quality alignments. AVAILABILITY AND IMPLEMENTATION: The Maligner software is written in C ++ and is available at https://github.com/LeeMendelowitz/maligner under the GNU General Public License. CONTACT: mpop@umiacs.umd.edu.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.