ECR Browser: a tool for visualizing and accessing data from comparisons of multiple vertebrate genomes - PubMed (original) (raw)

. 2004 Jul 1;32(Web Server issue):W280-6.

doi: 10.1093/nar/gkh355.

Affiliations

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

Ivan Ovcharenko et al. Nucleic Acids Res. 2004.

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.

PubMed Disclaimer

Figures

Figure 1

Figure 1

ECR Browser visualization of the Lim Domain Only 1 (LMO1) gene 46 kb locus in the human genome (UCSC freeze 16; NCBI Build 34). The conservation profiles of the human region in comparison with the mouse, rat, Fugu, tetraodon and zebra fish genomes are shown. The five genomes that were compared to the human region are plotted as horizontal layers of conservation diagrams and the small image icon at the right side of the plot represents the species corresponding to the alignment. Each layer contains a pip-type plot that consists of multiple short horizontal black lines. Each line represents an ungapped alignment, with the vertical height of the line describing the nucleotide identity underlying the alignment. Exons of the LMO1 gene are depicted in blue and yellow, with the blue bars depicting the exons that are protein coding while yellow bars depict the UTRs. The 5′–3′ orientation of the gene is given by arrow lines. A dark red bar on top of every layer provides an overview of the distribution of ECRs and is used to flag underlying regions of alignment. A conserved alignment is blue if it overlaps with a coding exon, yellow, UTR; pink, intron; red, intergenic region. The green bars at the bottom indicate repetitive elements in the base sequence. At the top of the browser display area quick-links to different chromosomes are offered, while the left bar represents a dynamic chromosomal map. The link to the UCSC Genome Browser (17) is also provided on the right side of the browser.

Figure 2

Figure 2

ECR Browser settings allow a flexible approach toward analysis of differently evolving genomic regions and dynamic choice of the plot and alignment settings.

Figure 3

Figure 3

‘Grab ECR’ feature—an access to the sequence, alignment and sequence analysis tools for a single ECR.

Figure 4

Figure 4

Synteny links in the ECR Browser—the human GATA3 gene generates syntenic alignments in mouse, rat and Fugu genomes (A). The alignments generated using the human (B), mouse (C) and rat (D) genomes as base sequences are displayed. In each case, four-genome alignments (human–mouse–rat–Fugu) are obtained, each with a different base genome. Notice the reverse transcriptional orientation of the GATA3 gene in the mouse genome, compared to that of humans and rats.

Figure 5

Figure 5

Genome alignment portal of the ECR Browser tool. Genomic sequences from any species that are submitted either as a FASTA file or automatically downloaded from GenBank by an accession number can be mapped and aligned to either human, mouse, rat or Fugu genomes (A). (B) A genome alignment of a cow sequence identified by accession number AC14683 with the human genome (hg16 freeze).

Similar articles

Cited by

References

    1. Loots G.G., Locksley,R.M., Blankespoor,C.M., Wang,Z.E., Miller,W., Rubin,E.M. and Frazer,K.A. (2000) Identification of a coordinate regulator of interleukins 4, 13, and 5 by cross-species sequence comparisons. Science, 288, 136–140. - PubMed
    1. Pennacchio L.A., Olivier,M., Hubacek,J.A., Cohen,J.C., Cox,D.R., Fruchart,J.C., Krauss,R.M. and Rubin,E.M. (2001) An apolipoprotein influencing triglycerides in humans and mice revealed by comparative sequencing. Science, 294, 169–173. - PubMed
    1. Elnitski L., Hardison,R.C., Li,J., Yang,S., Kolbe,D., Eswara,P., O'Connor,M.J., Schwartz,S., Miller,W. and Chiaromonte,F. (2003) Distinguishing regulatory DNA from neutral sites. Genome Res., 13, 64–72. - PMC - PubMed
    1. Elnitski L., Li,J., Noguchi,C.T., Miller,W. and Hardison,R. (2001) A negative cis-element regulates the level of enhancement by hypersensitive site 2 of the beta-globin locus control region. J. Biol. Chem., 276, 6289–6298. - PubMed
    1. Waterston R.H., Lindblad-Toh,K., Birney,E., Rogers,J., Abril,J.F., Agarwal,P., Agarwala,R., Ainscough,R., Alexandersson,M., An,P., et al. (2002) Initial sequencing and comparative analysis of the mouse genome. Nature, 420, 520–562. - PubMed

MeSH terms

Substances

LinkOut - more resources