Journal Article

r2cat: synteny plots and comparative assembly

Peter Husemann and Jens Stoye

in Bioinformatics

Volume 26, issue 4, pages 570-571
Published in print February 2010 | ISSN: 1367-4803
Published online December 2009 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btp690

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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

Journal Article.  1264 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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