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ZPicture: dynamic alignment and visualization tool for analyzing conservation profiles.

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.

SUBMITTER: Ovcharenko I

PROVIDER: S-EPMC353235 | biostudies-literature | 2004 Mar

REPOSITORIES: biostudies-literature

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zPicture: dynamic alignment and visualization tool for analyzing conservation profiles.

Ovcharenko Ivan I Loots Gabriela G GG Hardison Ross C RC Miller Webb W Stubbs Lisa L

Genome research 20040301 3

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 comp ...[more]

PMID: 14993211

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Project description:To date basic visualization of sequence alignments have largely focused on displaying per-site columns of nucleotide, or amino acid, residues along with associated frequency summarizations. The persistence of this tendency to the recent tools designed for viewing mapped read data indicates that such a perspective not only provides a reliable visualization of per-site alterations, but also offers implicit reassurance to the end-user in relation to data accessibility. However, the initial insight gained is limited, something that is especially true when viewing alignments consisting of many sequences representing differing factors such as location, date and subtype. A basic alignment viewer can have potential to increase initial insight through visual enhancement, whilst not delving into the realms of complex sequence analysis. We present CView, a visualizer that expands on the per-site representation of residues through the incorporation of a dynamic network that is based on the summarization of diversity present across different regions of the alignment. Within the network, nodes are based on the clustering of sequence fragments that span windows placed consecutively along the alignment. Edges are placed between nodes of neighbouring windows where they share sequence identification(s), i.e. different regions of the same sequence(s). Thus, if a node is selected on the network, then the relationship that sequences passing through that node have to other regions of diversity within the alignment can be observed through path tracing. In addition to augmenting visual insight, CView provides export features including variant summarization, per-site residue and kmer frequencies, consensus sequence, alignment dissection as well as clustering; each useful across a range of research areas. The software has been designed to be user friendly, intuitive and interactive. It is open source and an executable jar, source code, quick start, usage tutorial and test data are available (under the GNU General Public License) from https://sourceforge.net/projects/cview/.

Dataset Information

ZPicture: dynamic alignment and visualization tool for analyzing conservation profiles.

Publications

zPicture: dynamic alignment and visualization tool for analyzing conservation profiles.

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