ArticleProceedings of the National Academy of Sciences of the United States of America2005
EVOPRINTER, a multigenomic comparative tool for rapid identification of functionally important DNA.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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47 citing papers in PubMed, 67 citations in OpenAlex.
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- Mutational analysis of a Drosophila neuroblast enhancer governing nubbin expression during CNS development.Genesis (New York, N.Y. : 2000) · 2018Article
- Intestinal stem cell overproliferation resulting from inactivation of the APC tumor suppressor requires the transcription cofactors Earthbound and Erect wing.PLoS genetics · 2017Article
- Flavivirus and Filovirus EvoPrinters: New alignment tools for the comparative analysis of viral evolution.PLoS neglected tropical diseases · 2017Article
- Characterization of dFOXO binding sites upstream of the Insulin Receptor P2 promoter across the Drosophila phylogeny.PloS one · 2017Article
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- TargetOrtho: a phylogenetic footprinting tool to identify transcription factor targets.Genetics · 2014Article
- Flanking sequence context-dependent transcription factor binding in early Drosophila development.BMC bioinformatics · 2013Article
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- Hox proteins coordinate peripodial decapentaplegic expression to direct adult head morphogenesis in Drosophila.Developmental biology · 2012Article
- Engrailed cooperates directly with Extradenticle and Homothorax on a distinct class of homeodomain binding sites to repress sloppy paired.Developmental biology · 2012Article
- Comparative evaluation of intron prediction methods and detection of plant genome annotation using intron length distributions.Genomics & informatics · 2012Article
- Regulation of a duplicated locus: Drosophila sloppy paired is replete with functionally overlapping enhancers.Developmental biology · 2012Article
- Unique alterations of an ultraconserved non-coding element in the 3'UTR of ZIC2 in holoprosencephaly.PloS one · 2012Article
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4 authors at 2 institutions in 1 country.
Funding
Abstract
Here, we describe a multigenomic DNA sequence-analysis tool, evoprinter, that facilitates the rapid identification of evolutionary conserved sequences within the context of a single species. The evoprinter output identifies multispecies-conserved DNA sequences as they exist in a reference DNA. This identification is accomplished by superimposing multiple reference DNA vs. test-genome pairwise blat (blast-like alignment tool) readouts of the reference DNA to identify conserved nucleotides that are shared by all orthologous DNAs. evoprinter analysis of well characterized genes reveals that most, if not all, of the conserved sequences are essential for gene function. For example, analysis of orthologous genes that are shared by many vertebrates identifies conserved DNA in both protein-encoding sequences and noncoding cis-regulatory regions, including enhancers and mRNA microRNA binding sites. In Drosophila, the combined mutational histories of five or more species affords near-base pair resolution of conserved transcription factor DNA-binding sites, and essential amino acids are revealed by the nucleotide flexibility of their codon-wobble position(s). Conserved small peptide-encoding genes, which had been undetected by conventional gene-prediction algorithms, are identified by the codon-wobble signatures of invariant amino acids. Also, evoprinter allows one to assess the degree of evolutionary divergence between orthologous DNAs by highlighting differences between a selected species and the other test species.
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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.