zPicture: Dynamic alignment and visualization tool for analyzing conservation profiles

Ivan Ovcharenko, Gabriela G. Loots, Ross Cameron Hardison, Webb Miller, Lisa Stubbs

Research output: Contribution to journalArticle

104 Citations (Scopus)

Abstract

Comparative sequence analysis has evolved as an essential technique for identifying functional coding and noncoding elements conserved throughout evolution. Here, we introduce zPicture, an interactive Web-based sequence alignment and visualization tool for dynamically generating conservation profiles and identifying evolutionarily 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, in which 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 identified previously 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.

Original languageEnglish (US)
Pages (from-to)472-477
Number of pages6
JournalGenome research
Volume14
Issue number3
DOIs
StatePublished - Mar 1 2004

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Binding Sites
Genome
Molecular Sequence Annotation
Sequence Alignment
Sequence Analysis
Transcription Factors

All Science Journal Classification (ASJC) codes

  • Genetics

Cite this

Ovcharenko, Ivan ; Loots, Gabriela G. ; Hardison, Ross Cameron ; Miller, Webb ; Stubbs, Lisa. / zPicture : Dynamic alignment and visualization tool for analyzing conservation profiles. In: Genome research. 2004 ; Vol. 14, No. 3. pp. 472-477.
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zPicture : Dynamic alignment and visualization tool for analyzing conservation profiles. / Ovcharenko, Ivan; Loots, Gabriela G.; Hardison, Ross Cameron; Miller, Webb; Stubbs, Lisa.

In: Genome research, Vol. 14, No. 3, 01.03.2004, p. 472-477.

Research output: Contribution to journalArticle

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