title: OSLay: optimal syntenic layout of unfinished assemblies.
abstract: The whole genome shotgun approach to genome sequencing results in a collection of contigs that must be ordered and oriented to facilitate efficient gap closure. We present a new tool OSLay that uses synteny between matching sequences in a target assembly and a reference assembly to layout the contigs (or scaffolds) in the target assembly. The underlying algorithm is based on maximum weight matching. The tool provides an interactive visualization of the computed layout and the result can be imported into the assembly editing tool Consed to support the design of primer pairs for gap closure.
  
  
  BACKGROUND
  To enhance efficiency in the gap closure phase of a genome project it is crucial to know which contigs are adjacent in the target genome. Related genome sequences can be used to layout contigs in an assembly.
  
  
  BACKGROUND
  OSLay is freely available from: http://www-ab.informatik.unituebingen.de/software/oslay.
authors.affiliation: Center for Bioinformatics (ZBIT), Institute for Computer Science, Tübingen University, 72076 Tübingen, Germany. drichter@informatik.uni-tuebingen.de
authors.forename: Daniel C
authors.initials: DC
authors.lastname: Richter
authors.forename: Stephan C
authors.initials: SC
authors.lastname: Schuster
authors.forename: Daniel H
authors.initials: DH
authors.lastname: Huson
mesh_terms: D000465:Algorithms; D003196:Computer Graphics; D020451:Contig Mapping / Q000379:methods*; D017931:DNA Primers / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D014584:User-Computer Interface
chemical_list: D017931:DNA Primers