ChromoScope: A graphic interactive browser for E. coli data expressed in the NCBI data model

Jinghui Zhang, James Ostell, Kenneth Rudd

Research output: Chapter in Book/Report/Conference proceedingConference contribution

10 Citations (Scopus)

Abstract

An interactive graphic viewer, ChromoScope, was developed to explore scientific visualization of complicated genome data. Escherichia coli was selected as the test organism. An ASN.1 data set has been built for the entire E. coli chromosome, including a genetic map, a physical (ordered restriction) map, the alignment between the two maps, Kohara clones and some short repeat features. The E. coli sequence is modeled as a segmented sequence, incorporating both the sequence and the physical map data. The alignment between the contig and the published sequences is stored as sequence history, allowing direct access to the same sequence in the public databases. The alignment is displayed graphically, with both the sequence alignment and feature annotations. The alignment viewer also supports a detailed text display, providing information to resolution at residue level with annotated features.

Original languageEnglish
Title of host publicationProceedings of the Hawaii International Conference on System Sciences
EditorsJay F. Nunamaker, Ralph H.Jr. Sprague
Place of PublicationLos Alamitos, CA, United States
PublisherPubl by IEEE
Pages58-67
Number of pages10
Volume5
ISBN (Print)0818650907
StatePublished - Jan 1 1995
Externally publishedYes
EventProceedings of the 27th Hawaii International Conference on System Sciences (HICSS-27). Part 4 (of 5) - Wailea, HI, USA
Duration: Jan 4 1994Jan 7 1994

Other

OtherProceedings of the 27th Hawaii International Conference on System Sciences (HICSS-27). Part 4 (of 5)
CityWailea, HI, USA
Period1/4/941/7/94

Fingerprint

Escherichia coli
Data structures
Data visualization
Chromosomes
Genes
Display devices

ASJC Scopus subject areas

  • Software
  • Industrial and Manufacturing Engineering

Cite this

Zhang, J., Ostell, J., & Rudd, K. (1995). ChromoScope: A graphic interactive browser for E. coli data expressed in the NCBI data model. In J. F. Nunamaker, & R. H. J. Sprague (Eds.), Proceedings of the Hawaii International Conference on System Sciences (Vol. 5, pp. 58-67). Los Alamitos, CA, United States: Publ by IEEE.

ChromoScope : A graphic interactive browser for E. coli data expressed in the NCBI data model. / Zhang, Jinghui; Ostell, James; Rudd, Kenneth.

Proceedings of the Hawaii International Conference on System Sciences. ed. / Jay F. Nunamaker; Ralph H.Jr. Sprague. Vol. 5 Los Alamitos, CA, United States : Publ by IEEE, 1995. p. 58-67.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Zhang, J, Ostell, J & Rudd, K 1995, ChromoScope: A graphic interactive browser for E. coli data expressed in the NCBI data model. in JF Nunamaker & RHJ Sprague (eds), Proceedings of the Hawaii International Conference on System Sciences. vol. 5, Publ by IEEE, Los Alamitos, CA, United States, pp. 58-67, Proceedings of the 27th Hawaii International Conference on System Sciences (HICSS-27). Part 4 (of 5), Wailea, HI, USA, 1/4/94.
Zhang J, Ostell J, Rudd K. ChromoScope: A graphic interactive browser for E. coli data expressed in the NCBI data model. In Nunamaker JF, Sprague RHJ, editors, Proceedings of the Hawaii International Conference on System Sciences. Vol. 5. Los Alamitos, CA, United States: Publ by IEEE. 1995. p. 58-67
Zhang, Jinghui ; Ostell, James ; Rudd, Kenneth. / ChromoScope : A graphic interactive browser for E. coli data expressed in the NCBI data model. Proceedings of the Hawaii International Conference on System Sciences. editor / Jay F. Nunamaker ; Ralph H.Jr. Sprague. Vol. 5 Los Alamitos, CA, United States : Publ by IEEE, 1995. pp. 58-67
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