MIRA

MIRA assembles whole genome shotgun sequences and expressed sequence tags (ESTs) to reconstruct mRNA transcripts and detect and classify single nucleotide polymorphisms (SNPs) among transcript variants.

Key Features:

• Iterative Multipass Strategy: Uses an iterative multipass approach that prioritizes high-confidence regions and applies a fallback strategy for low-confidence regions during assembly.
• Handling of Similar Sequences: Manages large numbers of highly similar sequences without prior masking to preserve variant-specific information.
• Automatic Alignment Editing and Analysis: Performs automatic alignment editing by examining underlying trace data to refine alignments.
• SNP Detection and Classification: Detects and classifies SNPs with sensitivity down to one mutation per sequence.
• Utilization of Additional Sequencing Information: Incorporates base-error probabilities, template insert sizes, and strain information into assembly and variant analysis.
• Misassembly Detection and Resolution: Detects and resolves potential misassemblies to maintain assembly integrity.

Scientific Applications:

• Mutation Detection: Identifies mutations across different cell types via assembled transcripts and SNP calls.
• Transcript Similarity Analysis: Supports comparison of transcripts between organisms for evolutionary and comparative genomics studies.
• Oligo Design for Clinical Microarrays: Produces high-quality assembled sequences suitable for designing oligonucleotides for clinical microarray experiments.

Methodology:

Iterative multipass assembly prioritizing high-confidence regions with a fallback for low-confidence regions; automatic alignment editing using trace data; SNP detection and classification; integration of base-error probabilities, template insert sizes, and strain information; special handling of highly similar sequences without masking; and misassembly detection and resolution.