DOE Human Genome Program Contractor-Grantee Workshop VIII
February 27-March 2, 2000  Santa Fe, NM

56. Software to Support BAC Mapping

Cliff S. Han and Norman A. Doggett

Bioscience Division and DOE Joint Genome Institute, Los Alamos National Laboratory, Los Alamos, NM 87545

chan@telomere.lanl.gov

The LANL production mapping team has a major responsibility for supplying mapped BAC clones to the JGI's Production Sequencing Facility. Our approach involves the use of overgo probes to screen BAC filters and construct probe-content BAC maps. To facilitate this work we have developed and implemented several software programs. They are 1) Overgo selection program, 2) Automated contig assembly, and 3) Contig graphic draw.

Overgo selection program: The program is written to select overgos from a sequence. The program combines repeat screening and secondary structure screening with a nr Genbank search. Overgo sequences are checked for hairpins, selfdimers, heterodimers, and against RepBase and nr GenBank.

Automated contig assembly: The program assembling contigs automatically according to the input data. It can accept previously ordered backbone STS information as a constraint.

Contig graphic draw: The program is designed to draw a contig graphic map from probe(STS)-content map data that are presented in map order. The output is a Postscript III file. The file can be printed by draging onto the printer window or translated into a portable document format with Acrobat Distiller and viewed with Acrobat Reader. The input for the program is generated with the Automated contig assembly program or by a macro which can translate Excel data into the format for this program.

Supported by the US DOE, OBER under contract W-7405-ENG-36.