Algorithms and software tools for ordering clone libraries: Application to the mapping of the genome of Schizosaccharomyces pombe

Richard Mott, Andrei Grigoriev, Elmar Maier, Jorg Hoheisel, Hans Lehrach

Research output: Contribution to journalArticlepeer-review

66 Scopus citations

Abstract

A complete set of software tools to aid the physical mapping of a genome has been developed and successfully applied to the genomlc mapping of the fission yeast Schlzosaccharomyces pombe. Two approaches were used for ordering single-copy hybridisation probes: one was based on the simulated annealing algorithm to order all probes, and another on inferring the minimum-spanning subset of the probes using a heuristic filtering procedure. Both algorithms produced almost identical maps, with minor differences In the order of repetitive probes and those having identical hybridisation patterns. A separate algorithm fitted the clones to the established probe order. Approaches for handling experimental noise and repetitive elements are discussed. In addition to these programs and the database management software, tools for visualizing and editing the data are described. The issues of combining the Information from different libraries are addressed. Also, ways of handling multiple-copy probes and non-hybridisation data are discussed.

Original languageEnglish (US)
Pages (from-to)1965-1974
Number of pages10
JournalNucleic acids research
Volume21
Issue number8
DOIs
StatePublished - Apr 25 1993
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • Genetics

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