Gepard: a rapid and sensitive tool for creating dotplots on genome scale
Open Access
- 19 February 2007
- journal article
- research article
- Published by Oxford University Press (OUP) in Bioinformatics
- Vol. 23 (8), 1026-1028
- https://doi.org/10.1093/bioinformatics/btm039
Abstract
Summary: 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 Θ(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 Contact:krumsiek@in.tum.deKeywords
This publication has 10 references indexed in Scilit:
- tuple_plot: Fast pairwise nucleotide sequence comparison with noise suppressionBioinformatics, 2006
- The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomesNucleic Acids Research, 2004
- Replacing suffix trees with enhanced suffix arraysJournal of Discrete Algorithms, 2004
- Rapid and sensitive dot-matrix methods for genome analysisBioinformatics, 2004
- Versatile and open software for comparing large genomesGenome Biology, 2004
- Simple Linear Work Suffix Array ConstructionLecture Notes in Computer Science, 2003
- The PEDANT genome databaseNucleic Acids Research, 2003
- A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysisGene, 1995
- The Diagram, a Method for Comparing SequencesEuropean Journal of Biochemistry, 1970
- Locating gaps in amino acid sequences to optimize the homology between two proteinsBiochemical Genetics, 1969