zPicture and multi-zPicture

zPicture and multi-zPicture perform comparative genomic sequence alignments to identify evolutionarily conserved regions (ECRs) and enable transcription factor binding-site analysis across vertebrate and nonvertebrate genomes.

Key Features:

• Parameter-adjustable alignments: Generates conservation profiles with adjustable alignment parameters to accommodate varying phylogenetic distances and evolutionary rates.
• Conservation visualization and ECR identification: Visualizes conserved genomic regions and identifies conserved coding and noncoding elements, supporting detection of functional elements within complex loci.
• Transcription factor binding-site analysis (rVista integration): Integrates with rVista to map transcription factor binding sites within identified ECRs, exemplified by detection of GATA-1, NF-E2, and TAL1/E47 binding sites in ECRs within the HBB complex.
• UCSC Genome Browser integration: Retrieves sequences and gene annotations from the UCSC Genome Browser for recorded loci to support annotation-aware analyses.
• Cross-taxa applicability: Applies to vertebrate and nonvertebrate genomes, including microbial organisms.

Scientific Applications:

• Evolutionary conservation analysis: Detects evolutionarily conserved regions across species for comparative genomics studies.
• Regulatory element identification: Identifies candidate regulatory elements, including enhancers and transcription factor binding sites, within conserved regions.
• Functional genomics: Supports analysis of coding and noncoding element conservation to infer functional constraint and regulatory roles.
• Complex loci analysis: Discriminates functional ECRs within loci that contain extensive background conservation.

Methodology:

Built upon the blastz alignment program and implements pairwise alignments via zPicture and multiple alignments via multi-zPicture.