Projector 2

Projector 2 infers contig linkage from completed or draft genome sequences of related organisms and designs PCR primers to guide gap closure and improve genome assembly continuity.

Key Features:

• Template-based mapping: Uses completed or unfinished genome sequences from a related organism to map target contigs, infer adjacency, and prioritize gap closure.
• Gap-closure strategies: Supports PCR-based gap closure between contigs and provides automated primer design optimized for gap-filling workflows, with particular utility for prokaryotic genome assemblies.
• Repeat-masking and primer design: Masks repetitive elements to reduce spurious mappings and primer placement and accounts for unreliable sequence at contig ends and repeat-masked segments to improve amplification robustness.
• Multiplex PCR capabilities: Designs primer sets compatible with multiplex PCR for simultaneous amplification of multiple targets when multiple template fragments are used.
• High mapping success rates: Reports mapping success rates approaching 100% when using single or multiple template fragments in combination with repeat-masking.

Scientific Applications:

• Genome finishing: Improves contig ordering and accelerates gap closure to produce more continuous assemblies.
• Comparative genomics: Enables assembly completion guided by closely related species or strains to support comparative analyses.
• Evolutionary analyses: Facilitates evolutionary studies by providing more complete genomes for phylogenetic and population-level analyses.
• Functional annotation: Supports functional annotation by reducing assembly fragmentation that can obscure gene models, particularly in prokaryotic genomes.

Methodology:

Maps target contigs onto a related organism’s genome sequence, applies repeat-masking, and performs automated primer design to support PCR-based closure of inferred gaps.