r2cat: Synteny Plots and Comparative Assembly

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

Journal Article | Published | English

No fulltext has been uploaded

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.
Publishing Year

Cite this

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.
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.
This data publication is cited in the following publications:
This publication cites the following data publications:

46 Citations in Europe PMC

Data provided by Europe PubMed Central.

Challenges, Solutions, and Quality Metrics of Personal Genome Assembly in Advancing Precision Medicine.
Xiao W, Wu L, Yavas G, Simonyan V, Ning B, Hong H., Pharmaceutics 8(2), 2016
PMID: 27110816
Identifying Likely Transmission Pathways within a 10-Year Community Outbreak of Tuberculosis by High-Depth Whole Genome Sequencing.
Outhred AC, Holmes N, Sadsad R, Martinez E, Jelfs P, Hill-Cawthorne GA, Gilbert GL, Marais BJ, Sintchenko V., PLoS ONE 11(3), 2016
PMID: 26938641
Serotype 1 and 8 Pneumococci Evade Sensing by Inflammasomes in Human Lung Tissue.
Fatykhova D, Rabes A, Machnik C, Guruprasad K, Pache F, Berg J, Toennies M, Bauer TT, Schneider P, Schimek M, Eggeling S, Mitchell TJ, Mitchell AM, Hilker R, Hain T, Suttorp N, Hippenstiel S, Hocke AC, Opitz B., PLoS ONE 10(8), 2015
PMID: 26317436
Whole-genome comparative analysis of virulence genes unveils similarities and differences between endophytes and other symbiotic bacteria.
Lopez-Fernandez S, Sonego P, Moretto M, Pancher M, Engelen K, Pertot I, Campisano A., Front Microbiol 6(), 2015
PMID: 26074885
Complete Genome Sequence and Annotation of Corynebacterium singulare DSM 44357, Isolated from a Human Semen Specimen.
Merten M, Brinkrolf K, Albersmeier A, Kutter Y, Ruckert C, Tauch A., Genome Announc 3(2), 2015
PMID: 25814602
Draft Genome Sequence of Coxiella burnetii Strain Cb196, an Agent of Endocarditis in Saudi Arabia.
D'Amato F, Robert C, Azhar EI, Fournier PE, Raoult D., Genome Announc 2(6), 2014
PMID: 25428964
Complete Genome Sequence of Corynebacterium ureicelerivorans DSM 45051, a Lipophilic and Urea-Splitting Isolate from the Blood Culture of a Septicemia Patient.
Tippelt A, Albersmeier A, Brinkrolf K, Ruckert C, Fernandez-Natal I, Soriano F, Tauch A., Genome Announc 2(6), 2014
PMID: 25414509
Mycolic Acid Biosynthesis Genes in the Genome Sequence of Corynebacterium atypicum DSM 44849.
Tippelt A, Mollmann S, Albersmeier A, Jaenicke S, Ruckert C, Tauch A., Genome Announc 2(4), 2014
PMID: 25146145
IncH-type plasmid harboring bla CTX-M-15, bla DHA-1, and qnrB4 genes recovered from animal isolates.
Schluter A, Nordmann P, Bonnin RA, Millemann Y, Eikmeyer FG, Wibberg D, Puhler A, Poirel L., Antimicrob. Agents Chemother. 58(7), 2014
PMID: 24752252
Complete Genome Sequence of Corynebacterium falsenii DSM 44353 To Study the Evolution of Corynebacterium Cluster 3 Species.
Glaub A, Bomholt C, Gravermann K, Brinkrolf K, Albersmeier A, Ruckert C, Tauch A., Genome Announc 2(2), 2014
PMID: 24604654
Draft Genome Sequence of Pseudomonas moraviensis R28-S.
Hunter SS, Yano H, Loftie-Eaton W, Hughes J, De Gelder L, Stragier P, De Vos P, Settles ML, Top EM., Genome Announc 2(1), 2014
PMID: 24558233
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
Assembling contigs in draft genomes using reversals and block-interchanges.
Li CL, Chen KT, Lu CL., BMC Bioinformatics 14 Suppl 5(), 2013
PMID: 23734866
Draft genome sequence of the bean-nodulating Sinorhizobium fredii strain GR64.
Torres Tejerizo G, Lozano L, Gonzalez V, Bustos P, Romero D, Brom S., J. Bacteriol. 194(24), 2012
PMID: 23209231
First draft genome sequence of a strain from the genus Citricoccus.
Hayano-Kanashiro C, Lopez-Arredondo DL, Cruz-Morales P, Alcaraz LD, Olmedo G, Barona-Gomez F, Herrera-Estrella L., J. Bacteriol. 193(21), 2011
PMID: 21994924

8 References

Data provided by 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


0 Marked Publications

Open Data PUB

Web of Science

View record in Web of Science®


PMID: 20015948
PubMed | Europe PMC

Search this title in

Google Scholar