Fast algorithms for large-scale genome alignment and comparison.

By Arthur L. Delcher, Adam M. Phillippy, J. Carlton, Steven L. Salzberg. Nucleic Acids Research, 2002

1,090 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/d3a689f797042908ad4799dc2ae10168d36a96ab

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In Molecular Biology

Citations in the corpus

High-throughput sequence alignment using Graphics Processing Units (2007, methodology): “In particular, all programs in the NUCmer suite of programs that use the output of mummer, including those that extend the exact alignment seeds to larger inexact alignments, can take advantage of the GPU paralellization [4-6].”
Using MUMmer to Identify Similar Regions in Large Sequence Sets (2003, background): “Comparing Large Sequence Sets mon evolutionary phenomenon in these species, and that the inversions are nearly always symmetric about the origin of replication (Eisen et al., 2000).”
Gene sequences useful for predicting relatedness of whole genomes in bacteria. (2003, methodology): “Pairs of whole genomes were aligned by using the NUCMER application (Delcher et al., 2002) with the following parameters: breakLen=500, minCluster=40, diagFactor=0?”
The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes (2014, methodology): “To achieve this scalability, Parsnp is based on a suffix graph data structure for the rapid identification of maximal unique matches (MUMs), which serve as a common foundation to many pairwise [76,77,83] and multiple genome alignment tools [31-36].”
The comprehensive microbial resource (2000, background): “For example, a whole genome alignment between two bacteria using MUMmer (20) can be seen in a dotplot showing all the genes that are homologous between any two genomes the user selects; schematically, one can see large-scale conserved synteny as well as inversions and translocations in this display.”
Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system (2016, methodology): “Genomes were dereplicated by ﬁrst generating an alignment of all scaffolds within one genome individually against scaffolds of all other bins using NUCmer 62 at 98% nucleotide level or greater.”
Versatile and open software for comparing large genomes (2004, methodology): “More distantly related pairs of species, for example, Plasmodium falciparum and P. yoelii , fail to show DNA sequence similarity but do show large-scale similarity when their translated protein sequences are aligned, as described in earlier studies [7,8].”
A whole-genome assembly of the domestic cow, Bos taurus (2009, methodology): “First, we aligned with nucmer [17] the ends of contigs estimated to have a gap between them of <1 Kbp.”
Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis. (2012, background): “MUMmer [25] is less limited by database size, but is also much slower.”