Cited by 519Genomics and Phylogenetic StudiesGenomics and Chromatin DynamicsGenetics, Bioinformatics, and Biomedical Research

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ECR Browser: a tool for visualizing and accessing data from comparisons of multiple vertebrate genomes

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Ovcharenko, I., Nobrega, M. A., Loots, G. G., Stubbs, L.·2004·Nucleic Acids Research

DOI 10.1093/nar/gkh355PMC PMC441493

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Abstract

With an increasing number of vertebrate genomes being sequenced in draft or finished form, unique opportunities for decoding the language of DNA sequence through comparative genome alignments have arisen. However, novel tools and strategies are required to accommodate this large volume of genomic information and to facilitate the transfer of predictions generated by comparative sequence alignment to researchers focused on experimental annotation of genome function. Here, we present the ECR Browser, a tool that provides easy and dynamic access to whole genome alignments of human, mouse, rat and fish sequences. This web-based tool (http://ecrbrowser.dcode.org) provides the starting point for discovery of novel genes, identification of distant gene regulatory elements and prediction of transcription factor binding sites. The genome alignment portal of the ECR Browser also permits fast and automated alignments of any user-submitted sequence to the genome of choice. The interconnection of the ECR Browser with other DNA sequence analysis tools creates a unique portal for studying and exploring vertebrate genomes.

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Basic local alignment search tool
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“The R3HDML locus encodes a putative serine protease inhibitor belonging to the CRISP family of cysteine-rich secretory proteins, and contains evolutionarily conserved exonic and intronic regions bearing greater than 90% similarity to Rhesus macaque [89].”
Background
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Self-citation
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Krueger, K. C. (2009) · OhioLink ETD Center (Ohio Library and Information Network)
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Elbert, A. (2010) · TSpace (University of Toronto)
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“PIPMaker[3] provides percent identity plot(pip) and dot plot visualization result by computing the degree of match, so we can examine local alignment result closely[8].”
Background
DNA methylation analysis and identification of a novel antisense transcript in the Peg3 imprinted domain
Huang, J. M. (2009) · doi:10.31390/gradschool_dissertations.1070
Identification of Deleterious and Disease Alleles in a General Population and Preterm Labor Patients
Chun, S. (2012) · Open Scholarship Institutional Repository (Washington University in St. Louis) · doi:10.7936/k7tq5zjk
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Origins
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Peer Review #2 of "Analysis in silico of the functional interaction between WNT5A and YAP/TEAD signaling in cancer (v0.1)"
(2021) · PeerJ · doi:10.7287/peerj.10869v0.1/reviews/2
Peer Review #3 of "Analysis in silico of the functional interaction between WNT5A and YAP/TEAD signaling in cancer (v0.2)"
(2021) · PeerJ · doi:10.7287/peerj.10869v0.2/reviews/3
Peer Review #5 of "Analysis in silico of the functional interaction between WNT5A and YAP/TEAD signaling in cancer (v0.2)"
(2021) · PeerJ · doi:10.7287/peerj.10869v0.2/reviews/5
Peer Review #5 of "Analysis in silico of the functional interaction between WNT5A and YAP/TEAD signaling in cancer (v0.1)"
(2021) · PeerJ · doi:10.7287/peerj.10869v0.1/reviews/5
Peer Review #4 of "Analysis in silico of the functional interaction between WNT5A and YAP/TEAD signaling in cancer (v0.1)"
(2021) · PeerJ · doi:10.7287/peerj.10869v0.1/reviews/4
Caracterização de rearranjos cromossômicos citogeneticamente equilibrados associados a quadros clínicos
Fonseca, A. C. D. S. (2016) · Digital Library of Theses and Dissertations (Universidade de São Paulo) · doi:10.11606/t.41.2016.tde-05052016-112830
Peer Review #4 of "Analysis in silico of the functional interaction between WNT5A and YAP/TEAD signaling in cancer (v0.2)"
(2021) · PeerJ · doi:10.7287/peerj.10869v0.2/reviews/4
“The same region 134 was analyzed with the ECR browser (Ovcharenko et al., 2004) to search for similarity between 135 the WNT5A gene and the corresponding gene in the species indicated in the main text, retrieving 136 percent identity plots (PIPs) for evolutionary conserved regions (ECRs) and using…”
Method
PICALM
Lord, J., & Morgan, K. (2013) · Springer eBooks · doi:10.1007/978-1-4614-7309-1_4
Peer Review #1 of "Analysis in silico of the functional interaction between WNT5A and YAP/TEAD signaling in cancer (v0.1)"
(2021) · PeerJ · doi:10.7287/peerj.10869v0.1/reviews/1
Peer Review #3 of "Analysis in silico of the functional interaction between WNT5A and YAP/TEAD signaling in cancer (v0.1)"
(2021) · PeerJ · doi:10.7287/peerj.10869v0.1/reviews/3
The tissue-specificity associated region and motif of an emx2 downstream enhancer CNE2.04 in zebrafish
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Method
Improved serotonin neuron-specific viral vectors applicable for optogenetic manipulation and recording
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Liu, C., & Serra, R. A. (2025) · Gene Reports · doi:10.1016/j.genrep.2025.102252
Ectomesenchymal identity emerges via relief of Twist1 transcript destabilizationPreprint
Busby, L. C., Patrick, J. R., Lyons, L. W., & Martik, M. L. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.09.02.673848
“Candidate putative enhancer sequences were converted from the galGal3 genome assembly coordinates to galGal6 coordinates using the UCSD Genome Browser.”
Ythdc1‐p300‐Klf5 Complex‐Mediated Golgi Dysfunction Promotes Aortic Aneurysm
Wang, W., Song, Z., Bu, S., Liu, Y., Li, Q., Zhang, W., Sun, X., Zhang, X., Xiao, Y., Bo, D., et al. (2025) · Advanced Science · doi:10.1002/advs.202512116
Additional file 6 of Loss of RANBP3L leads to transformation of renal epithelial cells towards a renal clear cell carcinoma like phenotype
Chernyakov, D., Groß, A., Fischer, A., Bornkessel, N., Schultheiß, C., Gerloff, D., & Edemir, B. (2021) · Figshare · doi:10.6084/m9.figshare.14927033
Additional file 7 of Cis-regulatory analysis of Onecut1 expression in fate-restricted retinal progenitor cells
Patoori, S., Jean-Charles, N., Gopal, A., Sulaiman, S., Gopal, S., Wang, B., Souferi, B., & Emerson, M. M. (2020) · Figshare · doi:10.6084/m9.figshare.12010410
Additional file 9 of Loss of RANBP3L leads to transformation of renal epithelial cells towards a renal clear cell carcinoma like phenotype
Chernyakov, D., Groß, A., Fischer, A., Bornkessel, N., Schultheiß, C., Gerloff, D., & Edemir, B. (2021) · Figshare · doi:10.6084/m9.figshare.14927042
Additional file 8 of Cis-regulatory analysis of Onecut1 expression in fate-restricted retinal progenitor cells
Patoori, S., Jean-Charles, N., Gopal, A., Sulaiman, S., Gopal, S., Wang, B., Souferi, B., & Emerson, M. M. (2020) · Figshare · doi:10.6084/m9.figshare.12010413
Additional file 1 of Cis-regulatory analysis of Onecut1 expression in fate-restricted retinal progenitor cells
Patoori, S., Jean-Charles, N., Gopal, A., Sulaiman, S., Gopal, S., Wang, B., Souferi, B., & Emerson, M. M. (2020) · Figshare · doi:10.6084/m9.figshare.12010380
Additional file 5 of Cis-regulatory analysis of Onecut1 expression in fate-restricted retinal progenitor cells
Patoori, S., Jean-Charles, N., Gopal, A., Sulaiman, S., Gopal, S., Wang, B., Souferi, B., & Emerson, M. M. (2020) · Figshare · doi:10.6084/m9.figshare.12010401
Additional file 7 of Loss of RANBP3L leads to transformation of renal epithelial cells towards a renal clear cell carcinoma like phenotype
Chernyakov, D., Groß, A., Fischer, A., Bornkessel, N., Schultheiß, C., Gerloff, D., & Edemir, B. (2021) · Figshare · doi:10.6084/m9.figshare.14927036
Additional file 11 of Loss of RANBP3L leads to transformation of renal epithelial cells towards a renal clear cell carcinoma like phenotype
Chernyakov, D., Groß, A., Fischer, A., Bornkessel, N., Schultheiß, C., Gerloff, D., & Edemir, B. (2021) · Figshare · doi:10.6084/m9.figshare.14927012
Additional file 1 of Loss of RANBP3L leads to transformation of renal epithelial cells towards a renal clear cell carcinoma like phenotype
Chernyakov, D., Groß, A., Fischer, A., Bornkessel, N., Schultheiß, C., Gerloff, D., & Edemir, B. (2021) · Figshare · doi:10.6084/m9.figshare.14927018
Additional file 9 of Cis-regulatory analysis of Onecut1 expression in fate-restricted retinal progenitor cells
Patoori, S., Jean-Charles, N., Gopal, A., Sulaiman, S., Gopal, S., Wang, B., Souferi, B., & Emerson, M. M. (2020) · Figshare · doi:10.6084/m9.figshare.12010419

Authors: Ovcharenko, I., Nobrega, M. A., Loots, G. G., & Stubbs, L.
Affiliations: Lawrence Livermore National Laboratory (US)
Corresponding author: Ovcharenko, I.
ORCID: Ovcharenko, I.
Loots, G. G.
Stubbs, L.
Venue: Nucleic Acids Research
Publisher: Oxford University Press (OUP)
Published: 2004-07-01
Volume: 32
Issue: Web Server
Pages: W280-W286
ISSN: 0305-1048 (ISSN-L)
1362-4962
DOI: 10.1093/nar/gkh355
PMC: PMC441493
OpenAlex: W1981101983
Cited by: 519
References: 32
Citations by year: 2026: 6 · 2025: 9 · 2024: 10 · 2023: 8 · 2022: 13 · 2021: 32 · 2020: 23 · 2019: 19 · 2018: 27 · 2017: 21 · 2016: 24 · 2015: 21 · 2014: 23 · 2013: 42 · 2012: 40
FWCI: 8.17
Type: journal article
Language: en
Open access: bronze
doi.org
Locations: Nucleic Acids Research (publishedVersion)
Europe PMC (PubMed Central) (publishedVersion)
PubMed Central (publishedVersion)
PubMed (publishedVersion)
University of North Texas Digital Library (University of North Texas) (submittedVersion)
OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
Funders: U.S. Department of Energy (W-7405, -7405-ENG-48)
Biological and Environmental Research
Lawrence Livermore National Laboratory (W-7405-ENG 48, -7405-Eng-48)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genetics, Bioinformatics, and Biomedical Research
Keywords: vertebrate genomes, gene discovery, gene regulatory elements, transcription factor binding site prediction, genome annotation
MeSH terms: Animals, Binding Sites, Computer Graphics, Fishes, Humans, Regulatory Sequences, Nucleic Acid, Software, Transcription Factors, Sequence Alignment, Genome, Sequence Analysis, DNA, Systems Integration, Internet, Genomics, Synteny, Mice, Rats

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ECR Browser: a tool for visualizing and accessing data from comparisons of multiple vertebrate genomes

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