ASmodeler

ASmodeler models gene structures and alternative splicing by aligning mRNA, EST, and protein sequences to genomic maps to generate comprehensive gene models for transcriptome analysis.

Key Features:

• Alternative Splicing Modeling: Identifies and models alternative splicing events to represent splice variants and transcriptome complexity.
• Sequence Alignment: Aligns mRNA, EST, and protein sequences to genomic maps using BLAT with refinement by SIM4 to improve exon connectivity accuracy.
• Genome-based Clustering and Transcript Assembly: Integrates genome-based sequence clustering with transcript assembly procedures to assemble transcript models.
• Graph-Theoretic Analysis: Applies graph-theoretical methods to analyze exon connectivity and construct all possible gene models including splice variants.
• Integration with Existing Databases: Incorporates UniGene clusters and gene predictions from Genscan, Ensembl, and AceView (formerly Acembly) alongside user-supplied sequences.
• Multi-Species Support: Supports human, mouse, and rat genomes for comparative analyses.

Scientific Applications:

• Transcriptome Analysis: Enables reconstruction and analysis of alternative splicing patterns to characterize transcriptome diversity.
• Functional Genomics: Predicts splice variants and isoforms that can be investigated for distinct biological roles.
• Comparative Genomics: Facilitates comparison of splicing mechanisms and conservation across human, mouse, and rat genomes.

Methodology:

Combines genome-based sequence clustering with transcript assembly; aligns sequences to the genome using BLAT followed by refinement with SIM4; analyzes exon connectivity with graph-theoretic methods to construct comprehensive gene models including all possible splice variants.