OSLay: optimal syntenic layout of unfinished assemblies Export

@article{citeulike:2349830, abstract = {Summary: 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. Motivation: 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. Availability: OSLay is freely available from: http://www-ab.informatik.unituebingen.de/software/oslay Contact: drichter@informatik.uni-tuebingen.de 10.1093/bioinformatics/btm153}, author = {Richter, Daniel C. and Schuster, Stephan C. and Huson, Daniel H.}, citeulike-article-id = {2349830}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/bioinformatics/btm153}, citeulike-linkout-1 = {http://bioinformatics.oxfordjournals.org/content/23/13/1573.abstract}, citeulike-linkout-2 = {http://bioinformatics.oxfordjournals.org/content/23/13/1573.full.pdf}, citeulike-linkout-3 = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/13/1573}, citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/17463020}, citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=17463020}, day = {1}, doi = {10.1093/bioinformatics/btm153}, journal = {Bioinformatics}, keywords = {assembly, np-complete, oslay}, month = {July}, number = {13}, pages = {1573--1579}, posted-at = {2009-10-19 16:08:56}, priority = {2}, title = {OSLay: optimal syntenic layout of unfinished assemblies}, url = {http://dx.doi.org/10.1093/bioinformatics/btm153}, volume = {23}, year = {2007} }

TY - JOUR ID - citeulike:2349830 L3 - citeulike-article-id:2349830 N2 - Summary: 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. Motivation: 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. Availability: OSLay is freely available from: http://www-ab.informatik.unituebingen.de/software/oslay Contact: drichter@informatik.uni-tuebingen.de 10.1093/bioinformatics/btm153 IS - 13 JF - Bioinformatics EP - 1579 TI - OSLay: optimal syntenic layout of unfinished assemblies VL - 23 SP - 1573 KW - assembly KW - np-complete KW - oslay AU - Richter, Daniel AU - Schuster, Stephan AU - Huson, Daniel PY - 2007/07/01/ UR - http://dx.doi.org/10.1093/bioinformatics/btm153 ER -