VISTA

VISTA provides comparative analysis of genomic sequences to identify conserved elements and candidate regulatory enhancers across species.

Key Features:

• Phylo-VISTA: Organizes multi-sequence comparisons within a phylogenetic framework and computes similarity measures among DNA sequences at varying resolutions.
• AVID Alignment Method: Performs global alignments optimized for speed and memory to handle genomic regions up to megabases, supporting assembly comparisons and alignment of syntenic regions between species such as human and mouse.
• LAGAN and Multi-LAGAN Systems: Provide rapid global alignment of homologous genomic sequences, with Multi-LAGAN extending to multiple sequence alignments and demonstrating accuracy across distant species such as human, chicken, and fugu.
• VISTA Browser: Hosts pre-computed whole-genome alignments for large vertebrate genomes and other organisms and reports comparative analyses and functional annotations for genomic regions such as the human chromosome 5 interval encoding KIF3A.
• VISTA Enhancer Browser: Catalogs candidate enhancer elements in the human genome identified by comparative analysis and contains experimental validation data from transgenic mice covering over 250 tested DNA fragments with more than 100 confirmed tissue-specific enhancers.

Scientific Applications:

• Functional Genomics: Identification and characterization of conserved genomic elements across species.
• Comparative Genomics: Analysis of evolutionary relationships and conservation of genetic features across vertebrates and other organisms.
• Regulatory Element Discovery: Computational prediction and experimental validation of enhancer functions in the human genome, including tissue-specific activity tested in transgenic mice.

Methodology:

Integrates AVID, LAGAN, and Multi-LAGAN alignment algorithms and employs phylogenetic frameworks to organize and visualize sequence comparisons and to generate pre-computed whole-genome alignments.