Gepard: a rapid and sensitive tool for creating dotplots on genome scale

Jan Krumsiek; Roland Arnold; Thomas Rattei

doi:10.1093/bioinformatics/btm039

Gepard: a rapid and sensitive tool for creating dotplots on genome scale

Jan Krumsiek, Roland Arnold, Thomas Rattei

Cancer and Genomic Sciences

Research output: Contribution to journal › Article › peer-review

375 Citations (Scopus)

Abstract

UNLABELLED: Gepard provides a user-friendly, interactive application for the quick creation of dotplots. It utilizes suffix arrays to reduce the time complexity of dotplot calculation to Theta(m*log n). A client-server mode, which is a novel feature for dotplot creation software, allows the user to calculate dotplots and color them by functional annotation without any prior downloading of sequence or annotation data.

AVAILABILITY: Both source codes and executable binaries are available at http://mips.gsf.de/services/analysis/gepard

Original language	English
Pages (from-to)	1026-8
Number of pages	3
Journal	Bioinformatics
Volume	23
Issue number	8
DOIs	https://doi.org/10.1093/bioinformatics/btm039
Publication status	Published - 15 Apr 2007

Keywords

Algorithms
Chromosome Mapping
Computer Graphics
Sensitivity and Specificity
Software
User-Computer Interface
Journal Article

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10.1093/bioinformatics/btm039

Cite this

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abstract = "UNLABELLED: Gepard provides a user-friendly, interactive application for the quick creation of dotplots. It utilizes suffix arrays to reduce the time complexity of dotplot calculation to Theta(m*log n). A client-server mode, which is a novel feature for dotplot creation software, allows the user to calculate dotplots and color them by functional annotation without any prior downloading of sequence or annotation data.AVAILABILITY: Both source codes and executable binaries are available at http://mips.gsf.de/services/analysis/gepard",

keywords = "Algorithms, Chromosome Mapping, Computer Graphics, Sensitivity and Specificity, Software, User-Computer Interface, Journal Article",

author = "Jan Krumsiek and Roland Arnold and Thomas Rattei",

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doi = "10.1093/bioinformatics/btm039",

language = "English",

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KW - Algorithms

KW - Chromosome Mapping

KW - Computer Graphics

KW - Sensitivity and Specificity

KW - Software

KW - User-Computer Interface

KW - Journal Article

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JF - Bioinformatics

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ER -

Gepard: a rapid and sensitive tool for creating dotplots on genome scale

Abstract

Keywords

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