zPicture: Dynamic Alignment and Visualization Tool for Analyzing Conservation Profiles
- Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). Energy, Environment and Institutional Computing; Genome Biology Division
- Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). Genome Biology Division
- Pennsylvania State Univ., Univ. Park, PA (United States). Dept. of Computer Science and Engineering
- Pennsylvania State Univ., Univ. Park, PA (United States). Dept. of Computer Science and Engineering; Dept. of Biology
Comparative sequence analysis has evolved as an essential technique for identifying functional coding and noncoding elements conserved throughout evolution. Here we introduce zPicture (http://zpicture.dcode.org), an interactive web-based sequence alignment and visualization tool for dynamically generating conservation profiles and identifying evolutionary conserved regions (ECRs). zPicture is highly flexible because critical parameters can be modified interactively, allowing users to differentially predict ECRs in comparisons of sequences of different phylogenetic distances and evolutionary rates. We demonstrate the application of this module to identify a known regulatory element in the HOXD locus, where functional ECRs are difficult to discern against the highly conserved genomic background. zPicture also facilitates transcription factor binding site analysis via the rVISTA tool portal. We present an example of the HBB complex when zPicture/rVista combination specifically pinpoints to two ECRs containing GATA- 1, NF-E2 and TAL1/E47 binding sites that were previously identified as transcriptional enhancers. In addition, zPicture is linked to the UCSC Genome Browser allowing users to automatically extract sequences and gene annotations for any recorded locus. Finally, we describe how this tool can be efficiently applied to the analysis of nonvertebrate genomes including those of microbial organisms.
- Research Organization:
- Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
- Sponsoring Organization:
- USDOE
- DOE Contract Number:
- W-7405-ENG-48
- OSTI ID:
- 15016510
- Report Number(s):
- UCRL-JRNL-200708
- Journal Information:
- Published in: Genome Research, vol. 14, no. 3, April 1, 2004, pp. 472-477, Vol. 14, Issue 3
- Country of Publication:
- United States
- Language:
- English
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