Computer softwares for the search and entry of genome mapping data: Geneviewplus, locus-in and physical mapper

Shinsei Minoshima, Susumu Mitsuyama, Kazuhiko Kawasaki, Nobuyoshi Shimizu

Research output: Contribution to journalArticle

Abstract

Genome mapping data have been compiled into GDB (Genome Data Base) with international collaborative efforts. The GDB has become an indispensable international resource for human genome analysis. We have developed three new softwares which were designed for entry of raw mapping data, integration of various genome maps, and efficient use of GDB data. These systems have smooth graphical user interfaces and operate on a workstation with X-window. GeneViewPLUS is able to quickly search GDB data with easy operation; to accept both English and Japanese; to show the search results on graphical chromosome ideograms; to zoom-in to an interested region; and to show supplementary information of each map object. Locus-in is able to graphically display chromosome ideograms (800-band level) and zoom-in to a specific region of interest; to generate sub-windows regarding a specific region for entry and display of data including published data from GDB; to create new breakpoints to use as boundaries of sub-windows; to construct database by entering mapping objects into sub-windows; to show detailed information of each map object; and to manage the ownership of data. Physical Mapper is designed to draw various physical maps including contig map, restriction map, and STS map with easy operation using mouse; to coordinate these various maps in the same window on the common scale; and to manage a wide range scale from plasmid size (∼5 kb) to chromosome size (∼250 Mb).

Original languageEnglish (US)
Number of pages1
JournalJapanese Journal of Human Genetics
Volume41
Issue number1
StatePublished - Dec 1 1996

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Chromosome Mapping
Software
Genome
Databases
Chromosomes
Data Display
Ownership
Human Genome
Plasmids

All Science Journal Classification (ASJC) codes

  • Genetics(clinical)

Cite this

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title = "Computer softwares for the search and entry of genome mapping data: Geneviewplus, locus-in and physical mapper",
abstract = "Genome mapping data have been compiled into GDB (Genome Data Base) with international collaborative efforts. The GDB has become an indispensable international resource for human genome analysis. We have developed three new softwares which were designed for entry of raw mapping data, integration of various genome maps, and efficient use of GDB data. These systems have smooth graphical user interfaces and operate on a workstation with X-window. GeneViewPLUS is able to quickly search GDB data with easy operation; to accept both English and Japanese; to show the search results on graphical chromosome ideograms; to zoom-in to an interested region; and to show supplementary information of each map object. Locus-in is able to graphically display chromosome ideograms (800-band level) and zoom-in to a specific region of interest; to generate sub-windows regarding a specific region for entry and display of data including published data from GDB; to create new breakpoints to use as boundaries of sub-windows; to construct database by entering mapping objects into sub-windows; to show detailed information of each map object; and to manage the ownership of data. Physical Mapper is designed to draw various physical maps including contig map, restriction map, and STS map with easy operation using mouse; to coordinate these various maps in the same window on the common scale; and to manage a wide range scale from plasmid size (∼5 kb) to chromosome size (∼250 Mb).",
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Computer softwares for the search and entry of genome mapping data : Geneviewplus, locus-in and physical mapper. / Minoshima, Shinsei; Mitsuyama, Susumu; Kawasaki, Kazuhiko; Shimizu, Nobuyoshi.

In: Japanese Journal of Human Genetics, Vol. 41, No. 1, 01.12.1996.

Research output: Contribution to journalArticle

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