FPC

FPC assembles contigs from restriction fingerprinted clones by clustering clones using a probability-of-coincidence score derived from restriction fragment similarity to produce consensus band (CB) maps for large-scale sequencing and BAC fingerprint database assembly.

Key Features:

• Probability-of-coincidence scoring: Computes a probability-of-coincidence score from the similarity of restriction fragments produced by digesting clones with one or more restriction enzymes to evaluate clone overlap.
• Contig assembly and consensus band (CB) map generation: Constructs contigs of overlapping clones and generates a CB map as a consensus restriction-band representation for each contig.
• Clone coordinate assignment: Assigns coordinates to clones by aligning clone fingerprints to the consensus band (CB) map.
• Database management of contigs: Supports updating clone records and operations to merge, split, or delete contigs while associating markers with clones and mapping markers to contigs.
• Selection of sequence-ready clones: Identifies clones suitable for sequencing based on contig assembly and fingerprint information.
• Parallel processing: Provides a parallelized implementation that runs across multiple processors and servers and has been applied to assemble mammalian BAC fingerprint databases containing over 300,000 BAC fingerprints.

Scientific Applications:

• Assembly of restriction digest fingerprints: Assembles random restriction digest 'fingerprints' of overlapping genomic clones into contigs for genomic mapping.
• Large-scale sequencing projects: Facilitates clone selection and contig construction as part of large-scale sequencing and physical mapping efforts.
• Mammalian BAC fingerprint database assembly: Scales to assemble extensive BAC fingerprint datasets, including databases with hundreds of thousands of BAC fingerprints.

Methodology:

Computes probability-of-coincidence scores from restriction-fragment similarities, clusters clones into contigs based on those scores, generates consensus band (CB) maps for contigs, assigns clone coordinates by alignment to CB maps, and supports database operations and parallel execution across multiple processors/servers.