GAZE

GAZE predicts complete gene structures by integrating diverse evidence and assembling individual features into cohesive gene models using a dynamic programming algorithm.

Key Features:

• Dynamic programming assembly: Assembles individual gene components (features) into complete gene predictions using a dynamic programming algorithm.
• Posterior probability scoring: Computes posterior probabilities that each feature is part of a gene to score and select high-confidence assemblies.
• Externally supplied models and features: Accepts externally supplied input features and a validation/scoring model provided by the user.
• Pruning strategy: Employs a pruning strategy that maintains run-time complexity effectively linear with respect to sequence length.
• EST alignment integration: Incorporates similarity information from Expressed Sequence Tag (EST) alignments without requiring software modification.
• Nonstandard gene structures: Accommodates nonstandard gene structures such as trans-spliced genes in Caenorhabditis elegans.
• Signal and content sensors: Integrates signal and content sensor information alongside other biological evidence.

Scientific Applications:

• Comprehensive gene model construction: Integrates multiple evidence types to construct complete gene models from component features.
• Annotation of complex genomes: Supports annotation tasks that require combining diverse data sources and noncanonical gene structures.
• EST-supported gene refinement: Uses EST similarity information to refine and validate gene structure predictions.
• Detection of trans-splicing events: Enables prediction of trans-spliced genes as observed in Caenorhabditis elegans.

Methodology:

Uses a dynamic programming algorithm to assemble features into gene predictions; computes posterior probabilities for features; applies a pruning strategy to keep run-time effectively linear with sequence length; accepts externally supplied features and scoring/validation models; integrates EST similarity and signal/content sensor evidence.