Untitled

Abstract

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

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

“…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.…”

“…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.…”

“…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.…”

“…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.…”

“…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.…”