ArticleBMC genomics2008
Rapid detection and curation of conserved DNA via enhanced-BLAT and EvoPrinterHD analysis.
Article in BMC genomics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Role of the CASZ1 transcription factor in tissue development and disease.European journal of medical research · 2023Review
- Ultraconserved Non-coding DNA Within Diptera and Hymenoptera.G3 (Bethesda, Md.) · 2020Article
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- Mutational analysis of a Drosophila neuroblast enhancer governing nubbin expression during CNS development.Genesis (New York, N.Y. : 2000) · 2018Article
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- Flavivirus and Filovirus EvoPrinters: New alignment tools for the comparative analysis of viral evolution.PLoS neglected tropical diseases · 2017Article
- Regulation of UNC-130/FOXD-mediated mesodermal patterning in C. elegans.Developmental biology · 2016Article
- Gene Regulatory Mechanisms Underlying the Spatial and Temporal Regulation of Target-Dependent Gene Expression in Drosophila Neurons.PLoS genetics · 2015Article
- Article
- A view through a chromatin loop: insights into the ecdysone activation of early genes in Drosophila.Nucleic acids research · 2014Article
- Low-affinity transcription factor binding sites shape morphogen responses and enhancer evolution.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2013Article
- Article
- Using BLAT to find sequence similarity in closely related genomes.Current protocols in bioinformatics · 2012Article
- Use of a Drosophila genome-wide conserved sequence database to identify functionally related cis-regulatory enhancers.Developmental dynamics : an official publication of the American Association of Anatomists · 2012Article
- Identification of cis-Regulatory Elements in the dmyc Gene of Drosophila Melanogaster.Gene regulation and systems biology · 2012Article
- The Drosophila FTZ-F1 nuclear receptor mediates juvenile hormone activation of E75A gene expression through an intracellular pathway.The Journal of biological chemistry · 2011Article
- CASZ1b, the short isoform of CASZ1 gene, coexpresses with CASZ1a during neurogenesis and suppresses neuroblastoma cell growth.PloS one · 2011Article
- Molecular genetic analyses of polytene chromosome region 72A-D in Drosophila melanogaster reveal a gene desert in 72D.PloS one · 2011Article
- Molecular genetic manipulation of vector mosquitoes.Cell host & microbe · 2008Review
- Article
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Authors and funding
6 authors.
Funding
Abstract
backgroundMulti-genome comparative analysis has yielded important insights into the molecular details of gene regulation. We have developed EvoPrinter, a web-accessed genomics tool that provides a single uninterrupted view of conserved sequences as they appear in a species of interest. An EvoPrint reveals with near base-pair resolution those sequences that are essential for gene function.
resultsWe describe here EvoPrinterHD, a 2nd-generation comparative genomics tool that automatically generates from a single input sequence an enhanced view of sequence conservation between evolutionarily distant species. Currently available for 5 nematode, 3 mosquito, 12 Drosophila, 20 vertebrate, 17 Staphylococcus and 20 enteric bacteria genomes, EvoPrinterHD employs a modified BLAT algorithm [enhanced-BLAT (eBLAT)], which detects up to 75% more conserved bases than identified by the BLAT alignments used in the earlier EvoPrinter program. The new program also identifies conserved sequences within rearranged DNA, highlights repetitive DNA, and detects sequencing gaps. EvoPrinterHD currently holds over 112 billion bp of indexed genomes in memory and has the flexibility of selecting a subset of genomes for analysis. An EvoDifferences profile is also generated to portray conserved sequences that are uniquely lost in any one of the orthologs. Finally, EvoPrinterHD incorporates options that allow for (1) re-initiation of the analysis using a different genome's aligning region as the reference DNA to detect species-specific changes in less-conserved regions, (2) rapid extraction and curation of conserved sequences, and (3) for bacteria, identifies unique or uniquely shared sequences present in subsets of genomes.
conclusionEvoPrinterHD is a fast, high-resolution comparative genomics tool that automatically generates an uninterrupted species-centric view of sequence conservation and enables the discovery of conserved sequences within rearranged DNA. When combined with cis-Decoder, a program that discovers sequence elements shared among tissue specific enhancers, EvoPrinterHD facilitates the analysis of conserved sequences that are essential for coordinate gene regulation.
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