r2cat: Synteny Plots and Comparative Assembly
Husemann P, Stoye J (2010)
Bioinformatics 26(4): 570-571.
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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.
Erscheinungsjahr
2010
Zeitschriftentitel
Bioinformatics
Band
26
Ausgabe
4
Seite(n)
570-571
ISSN
1367-4803
eISSN
1460-2059
Page URI
https://pub.uni-bielefeld.de/record/1588556
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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. https://doi.org/10.1093/bioinformatics/btp690
Husemann, Peter, and Stoye, Jens. 2010. “r2cat: Synteny Plots and Comparative Assembly”. Bioinformatics 26 (4): 570-571.
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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Lu CL, Chen KT, Huang SY, Chiu HT., BMC Bioinformatics 15(), 2014
PMID: 25431302
Lu CL, Chen KT, Huang SY, Chiu HT., BMC Bioinformatics 15(), 2014
PMID: 25431302
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
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
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
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
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
Assembling contigs in draft genomes using reversals and block-interchanges.
Li CL, Chen KT, Lu CL., BMC Bioinformatics 14 Suppl 5(), 2013
PMID: 23734866
Li CL, Chen KT, Lu CL., BMC Bioinformatics 14 Suppl 5(), 2013
PMID: 23734866
Draft Genome Sequence of Bacillus atrophaeus UCMB-5137, a Plant Growth-Promoting Rhizobacterium.
Chan WY, Dietel K, Lapa SV, Avdeeva LV, Borriss R, Reva ON., Genome Announc 1(3), 2013
PMID: 23788535
Chan WY, Dietel K, Lapa SV, Avdeeva LV, Borriss R, Reva ON., Genome Announc 1(3), 2013
PMID: 23788535
Complete genome sequence and comparative analysis of Acetobacter pasteurianus 386B, a strain well-adapted to the cocoa bean fermentation ecosystem.
Illeghems K, De Vuyst L, Weckx S., BMC Genomics 14(), 2013
PMID: 23902333
Illeghems K, De Vuyst L, Weckx S., BMC Genomics 14(), 2013
PMID: 23902333
Genome annotation of Burkholderia sp. SJ98 with special focus on chemotaxis genes.
Kumar S, Vikram S, Raghava GP., PLoS One 8(8), 2013
PMID: 23940608
Kumar S, Vikram S, Raghava GP., PLoS One 8(8), 2013
PMID: 23940608
Draft genome sequence of the cellulolytic Clostridium thermocellum wild-type strain BC1 playing a role in cellulosic biomass degradation.
Koeck DE, Wibberg D, Koellmeier T, Blom J, Jaenicke S, Winkler A, Albersmeier A, Zverlov VV, Zverlov VV, Pühler A, Schwarz WH, Schlüter A., J Biotechnol 168(1), 2013
PMID: 23968723
Koeck DE, Wibberg D, Koellmeier T, Blom J, Jaenicke S, Winkler A, Albersmeier A, Zverlov VV, Zverlov VV, Pühler A, Schwarz WH, Schlüter A., J Biotechnol 168(1), 2013
PMID: 23968723
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
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
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
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
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
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
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
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
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
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
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
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
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