title: Maligner: a fast ordered restriction map aligner.
abstract: The 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.
  
  
  
  Here 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.
  
  
  
  The Maligner software is written in C ++ and is available at https://github.com/LeeMendelowitz/maligner under the GNU General Public License.
  
  
  
  mpop@umiacs.umd.edu.
authors.affiliation: Center for Bioinformatics and Computational Biology, Applied Math & Statistics, and Scientific Computation.
authors.forename: Lee M
authors.initials: LM
authors.lastname: Mendelowitz
authors.affiliation: Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, USA and the UW-Biotechnology Center, University of Wisconsin-Madison, WI 53706, USA.
authors.forename: David C
authors.initials: DC
authors.lastname: Schwartz
authors.affiliation: Center for Bioinformatics and Computational Biology, Applied Math & Statistics, and Scientific Computation, Department of Computer Science, University of Maryland, College Park, MD 20742, USA and.
authors.forename: Mihai
authors.initials: M
authors.lastname: Pop
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D016678:Genome; D015183:Restriction Mapping; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D012984:Software