r2cat: Synteny Plots and Comparative Assembly

Husemann P, Stoye J (2010)
Bioinformatics 26(4): 570-571.

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Zeitschriftenaufsatz | Veröffentlicht | Englisch
Abstract / Bemerkung
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.


Husemann P, Stoye J. r2cat: Synteny Plots and Comparative Assembly. Bioinformatics. 2010;26(4):570-571.
Husemann, P., & Stoye, J. (2010). r2cat: Synteny Plots and Comparative Assembly. Bioinformatics, 26(4), 570-571. doi:10.1093/bioinformatics/btp690
Husemann, P., and Stoye, J. (2010). r2cat: Synteny Plots and Comparative Assembly. Bioinformatics 26, 570-571.
Husemann, P., & Stoye, J., 2010. r2cat: Synteny Plots and Comparative Assembly. Bioinformatics, 26(4), p 570-571.
P. Husemann and J. Stoye, “r2cat: Synteny Plots and Comparative Assembly”, Bioinformatics, vol. 26, 2010, pp. 570-571.
Husemann, P., Stoye, J.: r2cat: Synteny Plots and Comparative Assembly. Bioinformatics. 26, 570-571 (2010).
Husemann, Peter, and Stoye, Jens. “r2cat: Synteny Plots and Comparative Assembly”. Bioinformatics 26.4 (2010): 570-571.

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Daten bereitgestellt von Europe PubMed Central.

Draft whole genome sequence of the cyanide-degrading bacterium Pseudomonas pseudoalcaligenes CECT5344.
Luque-Almagro VM, Acera F, Igeño MI, Wibberg D, Roldán MD, Sáez LP, Hennig M, Quesada A, Huertas MJ, Blom J, Merchán F, Escribano MP, Jaenicke S, Estepa J, Guijo MI, Martínez-Luque M, Macías D, Szczepanowski R, Becerra G, Ramirez S, Carmona MI, Gutiérrez O, Manso I, Pühler A, Castillo F, Moreno-Vivián C, Schlüter A, Blasco R., Environ Microbiol 15(1), 2013
PMID: 22998548
Establishment and interpretation of the genome sequence of the phytopathogenic fungus Rhizoctonia solani AG1-IB isolate 7/3/14.
Wibberg D, Jelonek L, Rupp O, Hennig M, Eikmeyer F, Goesmann A, Hartmann A, Borriss R, Grosch R, Pühler A, Schlüter A., J Biotechnol 167(2), 2013
PMID: 23280342
The genome sequence of Streptomyces lividans 66 reveals a novel tRNA-dependent peptide biosynthetic system within a metal-related genomic island.
Cruz-Morales P, Vijgenboom E, Iruegas-Bocardo F, Girard G, Yáñez-Guerra LA, Ramos-Aboites HE, Pernodet JL, Anné J, van Wezel GP, Barona-Gómez F., Genome Biol Evol 5(6), 2013
PMID: 23709624
Extraordinary expansion of a Sorangium cellulosum genome from an alkaline milieu.
Han K, Li ZF, Peng R, Zhu LP, Zhou T, Wang LG, Li SG, Zhang XB, Hu W, Wu ZH, Qin N, Li YZ., Sci Rep 3(), 2013
PMID: 23812535
Pangenomic study of Corynebacterium diphtheriae that provides insights into the genomic diversity of pathogenic isolates from cases of classical diphtheria, endocarditis, and pneumonia.
Trost E, Blom J, Soares Sde C, Huang IH, Al-Dilaimi A, Schröder J, Jaenicke S, Dorella FA, Rocha FS, Miyoshi A, Azevedo V, Schneider MP, Silva A, Camello TC, Sabbadini PS, Santos CS, Santos LS, Hirata R, Mattos-Guaraldi AL, Efstratiou A, Schmitt MP, Ton-That H, Tauch A., J Bacteriol 194(12), 2012
PMID: 22505676
A beginner's guide to eukaryotic genome annotation.
Yandell M, Ence D., Nat Rev Genet 13(5), 2012
PMID: 22510764
SIS: a program to generate draft genome sequence scaffolds for prokaryotes.
Dias Z, Dias U, Setubal JC., BMC Bioinformatics 13(), 2012
PMID: 22583530
A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs.
Swain MT, Tsai IJ, Assefa SA, Newbold C, Berriman M, Otto TD., Nat Protoc 7(7), 2012
PMID: 22678431
Draft genome sequence of the bean-nodulating Sinorhizobium fredii strain GR64.
Torres Tejerizo G, Lozano L, González V, Bustos P, Romero D, Brom S., J Bacteriol 194(24), 2012
PMID: 23209231
Targeted genome enrichment for efficient purification of endosymbiont DNA from host DNA.
Geniez S, Foster JM, Kumar S, Moumen B, Leproust E, Hardy O, Guadalupe M, Thomas SJ, Boone B, Hendrickson C, Bouchon D, Grève P, Slatko BE., Symbiosis 58(1-3), 2012
PMID: 23482460
Comparative analysis of two complete Corynebacterium ulcerans genomes and detection of candidate virulence factors.
Trost E, Al-Dilaimi A, Papavasiliou P, Schneider J, Viehoever P, Burkovski A, Soares SC, Almeida SS, Dorella FA, Miyoshi A, Azevedo V, Schneider MP, Silva A, Santos CS, Santos LS, Sabbadini P, Dias AA, Hirata R, Mattos-Guaraldi AL, Tauch A., BMC Genomics 12(), 2011
PMID: 21801446
Whole genome sequencing of environmental Vibrio cholerae O1 from 10 nanograms of DNA using short reads.
Pérez Chaparro PJ, McCulloch JA, Cerdeira LT, Al-Dilaimi A, Canto de Sá LL, de Oliveira R, Tauch A, de Carvalho Azevedo VA, Cruz Schneider MP, da Silva AL., J Microbiol Methods 87(2), 2011
PMID: 21871929
First draft genome sequence of a strain from the genus Citricoccus.
Hayano-Kanashiro C, López-Arredondo DL, Cruz-Morales P, Alcaraz LD, Olmedo G, Barona-Gómez F, Herrera-Estrella L., J Bacteriol 193(21), 2011
PMID: 21994924
Sequence Surveyor: leveraging overview for scalable genomic alignment visualization.
Albers D, Dewey C, Gleicher M., IEEE Trans Vis Comput Graph 17(12), 2011
PMID: 22034360
The complete genome sequence of Corynebacterium pseudotuberculosis FRC41 isolated from a 12-year-old girl with necrotizing lymphadenitis reveals insights into gene-regulatory networks contributing to virulence.
Trost E, Ott L, Schneider J, Schröder J, Jaenicke S, Goesmann A, Husemann P, Stoye J, Dorella FA, Rocha FS, Soares Sde C, D'Afonseca V, Miyoshi A, Ruiz J, Silva A, Azevedo V, Burkovski A, Guiso N, Join-Lambert OF, Kayal S, Tauch A., BMC Genomics 11(), 2010
PMID: 21192786

8 References

Daten bereitgestellt von Europe PubMed Central.

Basic local alignment search tool.
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ., J. Mol. Biol. 215(3), 1990
PMID: 2231712
ABACAS: algorithm-based automatic contiguation of assembled sequences.
Assefa S, Keane TM, Otto TD, Newbold C, Berriman M., Bioinformatics 25(15), 2009
PMID: 19497936
Phylogenetic comparative assembly.
Husemann P, Stoye J., Algorithms Mol Biol 5(), 2010
PMID: 20047659
BLAT--the BLAST-like alignment tool.
Kent WJ., Genome Res. 12(4), 2002
PMID: 11932250
Versatile and open software for comparing large genomes.
Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, Salzberg SL., Genome Biol. 5(2), 2004
PMID: 14759262
Efficient q-gram filters for finding all epsilon-matches over a given length
Rasmussen KR., 2006
OSLay: optimal syntenic layout of unfinished assemblies.
Richter DC, Schuster SC, Huson DH., Bioinformatics 23(13), 2007
PMID: 17463020
Projector 2: contig mapping for efficient gap-closure of prokaryotic genome sequence assemblies.
van Hijum SA, Zomer AL, Kuipers OP, Kok J., Nucleic Acids Res. 33(Web Server issue), 2005
PMID: 15980536


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