r2cat: synteny plots and comparative assembly

Summary: Recent parallel pyrosequencing methods and the increasing number of finished genomes encourage the sequencing and investigation of closely related strains. Although the sequencing itself becomes easier and cheaper with each machine generation, the finishing of the genomes remains difficult....

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Detalles Bibliográficos
Autores principales: Husemann, Peter, Stoye, Jens
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2010
Materias:
Applications Note
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2820676/
https://www.ncbi.nlm.nih.gov/pubmed/20015948
http://dx.doi.org/10.1093/bioinformatics/btp690
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author Husemann, Peter
Stoye, Jens
author_facet Husemann, Peter
Stoye, Jens
author_sort Husemann, Peter
collection PubMed
description Summary: Recent parallel pyrosequencing methods and the increasing number of finished genomes encourage the sequencing and investigation of closely related strains. Although the sequencing itself becomes easier and cheaper with each machine generation, the finishing of the genomes remains difficult. Instead of the desired whole genomic sequence, a set of contigs is the result of the assembly. In this applications note, we present the tool r2cat (related reference contig arrangement tool) that helps in the task of comparative assembly and also provides an interactive visualization for synteny inspection. Availability: http://bibiserv.techfak.uni-bielefeld.de/r2cat Contact: peter.husemann@cebitec.uni-bielefeld.de
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spelling pubmed-28206762010-02-12 r2cat: synteny plots and comparative assembly Husemann, Peter Stoye, Jens Bioinformatics Applications Note Summary: Recent parallel pyrosequencing methods and the increasing number of finished genomes encourage the sequencing and investigation of closely related strains. Although the sequencing itself becomes easier and cheaper with each machine generation, the finishing of the genomes remains difficult. Instead of the desired whole genomic sequence, a set of contigs is the result of the assembly. In this applications note, we present the tool r2cat (related reference contig arrangement tool) that helps in the task of comparative assembly and also provides an interactive visualization for synteny inspection. Availability: http://bibiserv.techfak.uni-bielefeld.de/r2cat Contact: peter.husemann@cebitec.uni-bielefeld.de Oxford University Press 2010-02-15 2009-12-16 /pmc/articles/PMC2820676/ /pubmed/20015948 http://dx.doi.org/10.1093/bioinformatics/btp690 Text en © The Author(s) 2009. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/2.0/uk/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Applications Note
Husemann, Peter
Stoye, Jens
r2cat: synteny plots and comparative assembly
title r2cat: synteny plots and comparative assembly
title_full r2cat: synteny plots and comparative assembly
title_fullStr r2cat: synteny plots and comparative assembly
title_full_unstemmed r2cat: synteny plots and comparative assembly
title_short r2cat: synteny plots and comparative assembly
title_sort r2cat: synteny plots and comparative assembly
topic Applications Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2820676/
https://www.ncbi.nlm.nih.gov/pubmed/20015948
http://dx.doi.org/10.1093/bioinformatics/btp690
work_keys_str_mv AT husemannpeter r2catsyntenyplotsandcomparativeassembly
AT stoyejens r2catsyntenyplotsandcomparativeassembly

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