28-way vertebrate alignment and conservation track in the UCSC Genome Browser.

By Webb Miller, Kate R. Rosenbloom, R. Hardison, Minmei Hou, James Taylor, Brian J. Raney, Richard Burhans, D. King, Robert Baertsch, Daniel J. Blankenberg and 16 more. Genome Research, 2007

303 citations recorded by the source corpus.

This article describes a set of alignments of 28 vertebrate genome sequences that is provided by the UCSC Genome Browser. The alignments can be viewed on the Human Genome Browser (March 2006 assembly) at http://genome.ucsc.edu, downloaded in bulk by anonymous FTP from http://hgdownload.cse.ucsc.edu/goldenPath/hg18/multiz28way, or analyzed with the Galaxy server at http://g2.bx.psu.edu. This article illustrates the power of this resource for exploring vertebrate and mammalian evolution, using three examples. First, we present several vignettes involving insertions and deletions within protein-coding regions, including a look at some human-specific indels. Then we study the extent to which start codons and stop codons in the human sequence are conserved in other species, showing that start codons are in general more poorly conserved than stop codons. Finally, an investigation of the phylogenetic depth of conservation for several classes of functional elements in the human genome reveals striking differences in the rates and modes of decay in alignability. Each functional class has a distinctive period of stringent constraint, followed by decays that allow (for the case of regulatory regions) or reject (for coding regions and ultraconserved elements) insertions and deletions.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/117ef21b2799ec2dc0a9ab83378c35234ab38db2

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In Molecular Biology

Citations in the corpus

Mash: fast genome and metagenome distance estimation using MinHash (2015, methodology): “Figure 4 compares this tree to an alignment-based phylogenetic tree model downloaded from the UCSC genome browser [26].”
Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps. (2008, background): “…Genome Initiative 2000), rice (Oryza sativa) (International Rice Genome Sequencing Project 2005), poplar (Populus trichocarpa) (Tuskan et al. 2006), grapevine (Vitis vinifera) (Jaillon et al. 2007), and papaya (Carica papaya) (Ming et al. 2008) have been sequenced, and more are in the pipeline.”
Upstream open reading frames cause widespread reduction of protein expression and are polymorphic among humans (2009, methodology): “RefSeq transcripts for human (hg18) and mouse (mm9) were obtained from the University of California, Santa Cruz (UCSC) Genome Browser Database (46) (accessed May 20, 2008), along with 28-vertebrate species alignments (47).”
Widespread Genomic Signatures of Natural Selection in Hominid Evolution (2009, methodology): “In high coverage genomes, the absence of long gaps is indicative of functional constraint [72], but in low-coverage genomes, long gaps may simply represent coverage gaps and are therefore less informative [24].”
progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement (2010, methodology): “browsers such as the UCSC browser [66], VISTA [67], and others”
Discovery and characterization of chromatin states for systematic annotation of the human genome (2010, methodology): “The conservation data were based on PhastCon conserved elements using the 44-way vertebrate alignmen”
ISMARA: automated modeling of genomic signals as a democracy of regulatory motifs (2014, methodology): “Briefly, we first obtained the topology of the tree from the UCSC Genome Browser[17].”
Most mammalian mRNAs are conserved targets of microRNAs. (2008, methodology): “Starting with a 28-way vertebrate whole-genome alignment that included 18 placental mammals and 10 other vertebrates (Miller et al. 2007), we extracted the human 3 UTRs and homologous regions from the 22 non-fish genomes.”