MAKER

MAKER annotates eukaryotic and prokaryotic genomes by integrating repeat identification, EST and protein alignments, ab initio gene predictions, and evidence synthesis to produce quality-indexed gene annotations for first- and second-generation sequencing projects.

Key Features:

• Portability and Configurability: Configurable and portable pipeline adaptable to different project needs and computational environments.
• Comprehensive Annotation Capabilities: Identifies genomic repeats, aligns expressed sequence tags (ESTs) and proteins to genomes, generates ab initio gene predictions, and synthesizes these data into evidence-based gene annotations with quality indices.
• Iterative Training: Automatically retrains gene-prediction algorithms using outputs from preliminary runs to improve subsequent gene models.
• Minimal Input Requirements: Operates with minimal input data to enable annotation when training or reference data are limited.
• Integration with GMOD and Apollo Genome Browser: Produces outputs compatible with Generic Model Organism Database (GMOD) creation and with viewing and editing in the Apollo Genome browser.
• MAKER2 Scalability: MAKER2 is multi-threaded and parallelized to scale for large second-generation sequencing datasets.
• Handling Limited Training Data: Can produce accurate annotations when training data are limited or absent.
• Utilization of mRNA-seq Data: Incorporates mRNA-seq data to improve annotation quality and to update legacy annotations.
• Quality Evaluation and Management: Evaluates annotation quality and identifies problematic regions for manual review.
• Legacy Annotation Updates: Manages and improves existing genome annotations to update legacy datasets.

Scientific Applications:

• Genome annotation of non-model organisms: Annotates genomes with limited prior genomic resources using integrated evidence and ab initio prediction.
• Schmidtea mediterranea annotation and SmedGD: Used to annotate Schmidtea mediterranea and to create the SmedGD genome database.
• Generation of community-accessible genome databases: Produces annotations and outputs suitable for building community genome databases from raw sequence and evidence.
• Updating legacy annotations: Updates and refines legacy annotations using mRNA-seq data and iterative retraining.
• Support for emerging model organism projects: Enables annotation in projects where pre-existing annotation resources are scarce.

Methodology:

Integrates repeat identification, EST and protein alignment, ab initio gene prediction, evidence synthesis with quality indices, and iterative retraining of gene-prediction algorithms; MAKER2 adds multi-threaded parallel processing and incorporation of mRNA-seq data.