An algorithm for the assembly of robust physical maps based on a combination of multi-level hybridization data and fingerprinting data

ODS2: a multiplatform software application for creating integrated physical and genetic maps

A contig map is a physical map that shows the native order of a library of overlapping genomic clones. One common method for creating such maps involves using hybridization to detect clone overlaps. False- positive and false-negative hybridization errors, the presence of chimeric clones, and gaps in library coverage lead to ambiguity and error in the clone order. Genomes with good genetic maps, such as Neurospora crassa, provide a means for reducing ambiguities and errors when constructing contig maps if clones can be anchored with genetic markers to the genetic map. A software application called ODS2 for creating contig maps based on clone-clone hybridization data is presented. This application is also designed to exploit partial ordering information provided by anchorage of clones to a genetic map. This information, along with clone-clone hybridization data, is used by a clone ordering algorithm and is represented graphically, allowing users to interactively align physical and genetic maps. ODS2 has a graphical user interface and is implemented entirely in Java, so it runs on multiple platforms. Other features include the flexibility of storing data in a local file or relational database and the ability to create full or minimum tiling contig maps.

Physical map and gene survey of the Ochrobactrum anthropi genome using bacterial artificial chromosome contigs

Bacterial artificial chromosome (BAC) clones are effective mapping and sequencing reagents for use with a wide variety of small and large genomes. This report describes research aimed at determining the genome structure of Ochrobactrum anthropi, an opportunistic human pathogen that has potential applications in biodegradation of hazardous organic compounds. A BAC library for O. anthropi was constructed that provides a 70-fold genome coverage based on an estimated genome size of 4.8 Mb. The library contains 3072 clones with an average insert size of 112 kb. High-density colony filters of the library were made, and a physical map of the genome was constructed using a hybridization without replacement strategy. In addition, 1536 BAC clones were fingerprinted with HindIII and analyzed using IMAGE and Fingerprint Contig software (FPC, Sanger Centre, U.K.). The FPC results supported the hybridization data, resulting in the formation of two major contigs representing the two major replicons of the O. anthropi genome. After determining a reduced tiling path, 138 BAC ends from the reduced tile were sequenced for a preliminary gene survey. A search of the public databases with the BLASTX algorithm resulted in 77 strong hits (E-value < 0.001), of which 89% showed similarity to a wide variety of prokaryotic genes. These results provide a contig-based physical map to assist the cloning of important genomic regions and the potential sequencing of the O. anthropi genome.