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FPC: a system for building contigs from restriction fingerprinted clones
C Soderlund1, I Longden, R Mott
1Sanger Centre, Hinxton, Cambridge, UK. cari@sanger.ac.uk
Computer Applications in the Biosciences : CABIOS
|November 21, 1997
Summary
Fingerprinted Contigs (FPC) software aids large-scale sequencing by assembling clones into contigs using restriction fragment data. It provides interactive tools for refining clone order and selecting sequence-ready clones efficiently.
Area of Science:
- Genomics
- Bioinformatics
Background:
- Large-scale sequencing requires efficient assembly of thousands of DNA clones into contigs.
- Restriction fragment analysis is a common method for fingerprinting clones and determining overlap probabilities.
Purpose of the Study:
- To introduce Fingerprinted Contigs (FPC), an interactive software tool for assembling restriction fingerprinted clones into contigs.
- To provide algorithmic support for rapid contig assembly and selection of minimal tiling paths for sequencing.
Main Methods:
- FPC clusters clones into contigs using an algorithm based on the probability of coincidence score of restriction fragments.
- It generates a consensus band (CB) map for each contig to visualize clone alignment and overlap.
- Interactive editing facilities allow users to refine clone coordinates and manage contigs.
Main Results:
- FPC successfully builds contigs and generates CB maps, facilitating clone order determination and visualization.
- The software supports updating databases, merging/splitting contigs, adding markers, and tracking sequencing status.
- FPC provides an integrated solution for assembling sequence-ready clones for large-scale projects.
Conclusions:
- FPC is an effective interactive program for assembling restriction fingerprinted clones into contigs.
- It streamlines the process of preparing clones for large-scale sequencing projects through visualization and editing tools.