Versatile and open software for comparing large genomes

Kurtz, Stefan; Phillippy, Adam M.; Delcher, Arthur L.; Smoot, Michael; Shumway, Martin; Antonescu, Corina; Salzberg, Steven L.

doi:10.1186/gb-2004-5-2-r12

Cited by 4,877 publications

(3,037 citation statements)

References 34 publications

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“…These gaps account for 2.9 Mb, or 0.1%, of the genome. By aligning the RefSeq assembly to PICR using MUMmer3.0 [Kurtz et al, 2004], we identified missing sequence for 125,812 (76%) of the RefSeq gaps (Figure 3.b and Methods). Sequence for a subset of RefSeq gaps was not identified in the PICR metassembly.…”

Section: Resultsmentioning

confidence: 99%

“…For each metassembly, one assembly is selected as the primary assembly. The scaffolds of a second assembly are subsequently mapped to the primary scaffolds using NUCmer [Kurtz et al, 2004]. A CE-statistic, based on the distance of mate-pair reads, is computed for both assemblies.…”

Section: Methodsmentioning

confidence: 99%

“…If at least 90% of the 1 kb region of a scaffold showed a normalized coverage between 0.5 and 2 of the same chromosome, the scaffold was assigned to this chromosome. Scaffolds assigned to the pooled chromosome 9 and 10 library and all unassigned scaffolds were mapped to the mouse genome using NUCmer [Kurtz et al, 2004]. Yang et al [Yang et al, 2000] and Wlaschin et al [Wlaschin and Hu, 2007] described the localization of the hamster chromosomes on the mouse chromosomes.…”

Section: Methodsmentioning

confidence: 99%

“…The resulting transcripts were aligned to the previously published hamster transcriptome assembly [Lewis et al, 2013], which had used Trinity v. r2011-08-20. NUCmer [Kurtz et al, 2004] was used for the alignment with default parameters. 91,027 transcripts were found in both transcriptomes and used as evidence for gene prediction within Maker.…”

Section: Methodsmentioning

confidence: 99%

“…We aligned the Chinese hamster RefSeq genome sequence to the PICR genome sequence using NUCmer [Kurtz et al, 2004] to identify gap sequence (see Supplementary Figure S9). Briefly, NUCmer clusters a set of maximally exact matches as an anchor, and then extends alignments between the clustered matches.…”

Section: Methodsmentioning

confidence: 99%

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A reference genome of the Chinese hamster based on a hybrid assembly strategy

Rupp

MacDonald

et al. 2018

Biotech & Bioengineering

103

121

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Accurate and complete genome sequences are essential in biotechnology to facilitate genome-based cell engineering efforts. The current genome assemblies for Cricetulus griseus, the Chinese hamster, are fragmented and replete with gap sequences and misassemblies, consistent with most short-read based assemblies. Here, we completely resequenced C. griseus using Single Molecule Real Time (SMRT) sequencing and merged this with Illumina-based assemblies. This generated a more contiguous and complete genome assembly than either technology alone, reducing the number of scaffolds by >28-fold, with 90% of the sequence in the 122 longest scaffolds. Most genes are now found in single scaffolds, including up- and downstream regulatory elements, enabling improved study of noncoding regions. With >95% of the gap sequence filled, important CHO cell mutations have been detected in draft assembly gaps. This new assembly will be an invaluable resource for continued basic and pharmaceutical research.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

See 3 more Smart Citations

A reference genome of the Chinese hamster based on a hybrid assembly strategy

Rupp

MacDonald

et al. 2018

Biotech & Bioengineering

103

121

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Repeatfinding

Sucgang¹

2005

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

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Finding repeats in biological sequences is a necessary first step in recognizing patterns and biologically relevant motifs. Given the inexact nature of biological repeats, the software required to detect, identify, classify, and curate them have grown not only in variety but in sophistication as well, accommodating increases both in amount of data and available computing power. Open source and free‐for‐academic‐use programs implementing repeat finding algorithms, as well as databases that curate known biological repeat motifs are surveyed in this section.

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Three‐base periodicity of sites of sequence variation in Pseudomonas aeruginosa and Staphylococcus aureus core genomes

et al. 2016

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The three-base periodicity property is characteristic of protein-coding sequences. Here, we report on three-base periodicity of sequence variation in the core genome of bacteria. Single nucleotide polymorphism (SNP) syntenies were extracted from pairwise genome alignments of 41 Staphylococcus aureus or 20 Pseudomonas aeruginosa strains. The length of fragment pairs with identical nucleotides at all SNP positions showed a length-dependent overrepresentation of multiples of three nucleotides at corresponding codon positions of the AT-rich S. aureus and the GC-rich P. aeruginosa. Three-base SNP periodicity seems to be a characteristic feature of the tightly arranged bacterial core genome.

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Versatile and open software for comparing large genomes

Abstract: The newest version of MUMmer easily handles comparisons of large eukaryotic genomes at varying evolutionary distances, as demonstrated by applications to multiple genomes.

Cited by 4,877 publications

References 34 publications

A reference genome of the Chinese hamster based on a hybrid assembly strategy

A reference genome of the Chinese hamster based on a hybrid assembly strategy

Repeatfinding

Three‐base periodicity of sites of sequence variation in Pseudomonas aeruginosa and Staphylococcus aureus core genomes

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