C-Sibelia: an easy-to-use and highly accurate tool for bacterial genome comparison
TLDR
C-Sibelia is a highly accurate and easy-to-use software tool for comparing two closely related bacterial genomes, which can be presented as either finished sequences or fragmented assemblies.Abstract:
We present C-Sibelia, a highly accurate and easy-to-use software tool for comparing two closely related bacterial genomes, which can be presented as either finished sequences or fragmented assemblies. C-Sibelia takes as input two FASTA files and produces: (1) a VCF file containing all identified single nucleotide variations and indels; (2) an XMFA file containing alignment information. The software also produces Circos diagrams visualizing high level genomic architecture for rearrangement analyses. C-Sibelia is a part of the Sibelia comparative genomics suite, which is freely available under the GNU GPL v.2 license at http://sourceforge.net/projects/sibelia-bio. C-Sibelia is compatible with Unix-like operating systems. A web-based version of the software is available at http://etool.me/software/csibelia.read more
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References
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Journal ArticleDOI
Circos: An information aesthetic for comparative genomics
Martin Krzywinski,Jacqueline E. Schein,Inanc Birol,Joseph M. Connors,Randy D. Gascoyne,Doug Horsman,Steven J.M. Jones,Marco A. Marra +7 more
TL;DR: Circos uses a circular ideogram layout to facilitate the display of relationships between pairs of positions by the use of ribbons, which encode the position, size, and orientation of related genomic elements.
Journal ArticleDOI
A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3
Pablo Cingolani,Adrian E. Platts,Le Lily Wang,M. Coon,Tung T. Nguyen,Luan Wang,Susan Land,Xiangyi Lu,Douglas M. Ruden +8 more
TL;DR: It appears that the 5′ and 3′ UTRs are reservoirs for genetic variations that changes the termini of proteins during evolution of the Drosophila genus.
Journal ArticleDOI
Versatile and open software for comparing large genomes
Stefan Kurtz,Adam M. Phillippy,Arthur L. Delcher,Michael E. Smoot,Martin Shumway,Corina Antonescu,Steven L. Salzberg +6 more
TL;DR: The newest version of MUMmer easily handles comparisons of large eukaryotic genomes at varying evolutionary distances, as demonstrated by applications to multiple genomes.
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progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement
TL;DR: A new method to align two or more genomes that have undergone rearrangements due to recombination and substantial amounts of segmental gain and loss is described, demonstrating high accuracy in situations where genomes have undergone biologically feasible amounts of genome rearrangement, segmental loss and loss.
Journal ArticleDOI
BLAST 2 Sequences, a new tool for comparing protein and nucleotide sequences.
TL;DR: 'BLAST 2 Sequences', a new BLAST-based tool for aligning two protein or nucleotide sequences, is described, utilizing the BLAST algorithm for pairwise DNA-DNA or protein-protein sequence comparison.