PanGEA

PanGEA maps 454 ESTs to genes and genomes and quantifies SNPs and allele-specific expression to characterize gene expression and genetic variation.

Key Features:

• Mapping and expression profiling: Maps 454 ESTs to specific genes or whole genomes and visualizes comprehensive gene expression profiles.
• SNP identification and allele-specific expression: Identifies single nucleotide polymorphisms (SNPs) and quantifies allele-specific gene expression from 454 sequencing data.
• Algorithmic enhancement: Implements a modified Smith-Waterman algorithm to correct homopolymer length estimation errors associated with 454 sequencing technology.
• High-throughput data handling: Processes large 454 sequencing datasets suitable for high-throughput expression analyses.

Scientific Applications:

• Allele-specific expression analysis: Enables precise identification and quantification of allele-specific expression for studies of genetic regulation.
• Genetic disorder research: Supports investigation of SNPs and allele-specific effects implicated in genetic disorders.
• Evolutionary biology: Facilitates evolutionary biology studies by enabling comparison of SNP patterns and allele-specific expression.
• Personalized medicine: Contributes to personalized medicine by linking genetic variation to gene expression differences.

Methodology:

Integrates 454 sequencing data with bioinformatics algorithms to map ESTs to genes/genomes, detect SNPs, quantify allele-specific expression, and applies a modified Smith-Waterman algorithm to address homopolymer length estimation in 454 reads.