BEAP

BEAP reconstructs extended genomic contigs by recursively BLASTing nucleotide databases and assembling overlapping sequences with CAP3 to extend partial sequences (e.g., ESTs or partial gene segments) for fine-mapping, SNP discovery, and positional cloning in species with incomplete genome assemblies.

Key Features:

• Integration of BLAST and CAP3: Combines BLAST nucleotide database searching with CAP3 sequence assembly to retrieve and assemble overlapping sequences into longer contigs.
• Recursive Sequence Extension: Recursively blasts from an initial short fragment (such as an EST or partial gene segment) to identify sequences that overlap directly or indirectly with the primer sequence to extend the original sequence.
• Contig Construction: Assembles retrieved overlapping sequences into contigs representing localized genomic regions for downstream analyses including SNP prediction.
• Template-based Cross-species Querying: Uses a completed genome or user-defined template sequences as queries to exploit homology between template and target species to close gaps or extend contigs.
• Application in Fine-Mapping and Positional Cloning: Generates sequences suitable for discovering orthologous genes and positional cloning, demonstrated by generating genomic template sequences for the Angus dwarfism mutation.
• User-Defined Templates: Requires selection of appropriate template sequences based on comparative mapping evidence such as radiation hybrid maps to tailor searches to specific research questions.

Scientific Applications:

• Fine-mapping: Extends local genomic sequence around loci of interest to support high-density SNP marker development and positional candidate gene identification.
• SNP discovery: Produces extended contigs that enable prediction and validation of single nucleotide polymorphisms for marker development.
• Linkage disequilibrium analysis: Provides contiguous sequence context for analyses of linkage disequilibrium and haplotype structure.
• Positional cloning and orthology inference: Reconstructs genomic regions and orthologous gene sequences across species to support positional cloning efforts, including use cases such as the Angus dwarfism mutation.

Methodology:

Select a completed genome or user-defined template (e.g., guided by radiation hybrid maps), recursively BLAST nucleotide databases starting from a short fragment (EST or partial gene), retrieve directly and indirectly overlapping sequences, and assemble retrieved sequences into contigs using CAP3, assuming sufficient homology between template and target species.