ArticleGenome research2004
Automated whole-genome multiple alignment of rat, mouse, and human.
Article in Genome research, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
40 citing papers in PubMed.
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- The invasive MED/Q Bemisia tabaci genome: a tale of gene loss and gene gain.BMC genomics · 2018Article
- Efficient and rapid generation of large genomic variants in rats and mice using CRISMERE.Scientific reports · 2017Article
- STAR3D: a stack-based RNA 3D structural alignment tool.Nucleic acids research · 2015Article
- Whole-genome sequence of the Tibetan frog Nanorana parkeri and the comparative evolution of tetrapod genomes.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Repression of global protein synthesis by Eif1a-like genes that are expressed specifically in the two-cell embryos and the transient Zscan4-positive state of embryonic stem cells.DNA research : an international journal for rapid publication of reports on genes and genomes · 2013Article
- The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan.Nature genetics · 2013Article
- C-Sibelia: an easy-to-use and highly accurate tool for bacterial genome comparison.F1000Research · 2013Article
- The endocrine stress response is linked to one specific locus on chromosome 3 in a mouse model based on extremes in trait anxiety.BMC genomics · 2012Article
- Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory.BMC bioinformatics · 2012Article
- Long identical multispecies elements in plant and animal genomes.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
- Profiling trait anxiety: transcriptome analysis reveals cathepsin B (Ctsb) as a novel candidate gene for emotionality in mice.PloS one · 2011Article
- Feature amplified voting algorithm for functional analysis of protein superfamily.BMC genomics · 2010Article
- Cgaln: fast and space-efficient whole-genome alignment.BMC bioinformatics · 2010Article
- Parameters for accurate genome alignment.BMC bioinformatics · 2010Article
- Elucidating genome structure evolution by analysis of isoapostatic gene clusters using statistics of variance of gene distances.Genome biology and evolution · 2009Article
- Binding sites for ETS family of transcription factors dominate the promoter regions of differentially expressed genes in abdominal aortic aneurysms.Circulation. Cardiovascular genetics · 2009Article
- Genetics of Sex-linked yellow in the Syrian hamster.Genetics · 2009Article
- Multiple whole-genome alignments without a reference organism.Genome research · 2009Article
- ABT-510 is an effective chemopreventive agent in the mouse 4-nitroquinoline 1-oxide model of oral carcinogenesis.Cancer prevention research (Philadelphia, Pa.) · 2009Article
Corrections and comments
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We have built a whole-genome multiple alignment of the three currently available mammalian genomes using a fully automated pipeline that combines the local/global approach of the Berkeley Genome Pipeline and the LAGAN program. The strategy is based on progressive alignment and consists of two main steps: (1) alignment of the mouse and rat genomes, and (2) alignment of human to either the mouse-rat alignments from step 1, or the remaining unaligned mouse and rat sequences. The resulting alignments demonstrate high sensitivity, with 87% of all human gene-coding areas aligned in both mouse and rat. The specificity is also high: <7% of the rat contigs are aligned to multiple places in human, and 97% of all alignments with human sequence >100 kb agree with a three-way synteny map built independently, using predicted exons in the three genomes. At the nucleotide level <1% of the rat nucleotides are mapped to multiple places in the human sequence in the alignment, and 96.5% of human nucleotides within all alignments agree with the synteny map. The alignments are publicly available online, with visualization through the novel Multi-VISTA browser that we also present.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.