The DOI matches its Crossref record; 10 of the 10 references it cites were found in a registry or an index.
Gepard: a rapid and sensitive tool for creating dotplots on genome scale
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.de
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Cites
Versatile and open software for comparing large genomes
Kurtz, S., Phillippy, A., Delcher, A. L., Smoot, M., Shumway, M., Antonescu, C., & Salzberg, S. L. (2004) · Genome Biology · doi:10.1186/gb-2004-5-2-r12 · Cited by 5,254
Ruepp, A. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh894 · Cited by 1,133
Sonnhammer, E. L. L., & Durbin, R. (1995) · Gene · doi:10.1016/0378-1119(95)00714-8 · Cited by 777
Replacing suffix trees with enhanced suffix arrays
Abouelhoda, M. I., Kurtz, S., & Ohlebusch, E. (2004) · Journal of Discrete Algorithms · doi:10.1016/s1570-8667(03)00065-0 · Cited by 668
Simple Linear Work Suffix Array Construction
Kärkkäinen, J., & Sanders, P. (2003) · Lecture Notes in Computer Science · doi:10.1007/3-540-45061-0_73 · Cited by 404
The Diagram, a Method for Comparing Sequences: Its Use with Amino Acid and Nucleotide Sequences
Gibbs, A. J., & Mcintyre, G. A. (1970) · European Journal of Biochemistry · doi:10.1111/j.1432-1033.1970.tb01046.x · Cited by 313
Frishman, D., Mokrejs, M., Kosykh, D., Kastenmüller, G., Kolesov, G., Zubrzycki, I., Gruber, C., Geier, B., Kaps, A., Albermann, K., et al. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg005 · Cited by 141
Rapid and sensitive dot-matrix methods for genome analysis
Huang, Y. L., & Zhang, L. (2004) · Bioinformatics · doi:10.1093/bioinformatics/btg429 · Cited by 54
Locating gaps in amino acid sequences to optimize the homology between two proteins
Fitch, W. M. (1969) · Biochemical Genetics · doi:10.1007/bf00520346 · Cited by 49
tuple_plot: Fast pairwise nucleotide sequence comparison with noise suppression
Szafranski, K., Jahn, N., & Platzer, M. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl277 · Cited by 16
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Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data
Chin, C.-S., Alexander, D. H., Marks, P., Klammer, A. A., Drake, J., Heiner, C., Clum, A., Copeland, A., Huddleston, J., Eichler, E. E., et al. (2013) · Nature Methods · doi:10.1038/nmeth.2474 · Cited by 4,029
Towards complete and error-free genome assemblies of all vertebrate species
Rhie, A., McCarthy, S. A., Fedrigo, O., Damas, J., Formenti, G., Koren, S., Uliano-Silva, M., Chow, W., Fungtammasan, A., Kim, J., et al. (2021) · Nature · doi:10.1038/s41586-021-03451-0 · Cited by 3,097
Towards complete and error-free genome assemblies of all vertebrate species
Rhie, A., McCarthy, S. A., Fedrigo, O., Damas, J., Formenti, G., Koren, S., Uliano-Silva, M., Chow, W., Fungtammasan, A., Gedman, G. L., et al. (2020) · doi:10.1101/2020.05.22.110833 · Cited by 3,097
Insights into Land Plant Evolution Garnered from the Marchantia polymorpha Genome
Bowman, J. L., Kohchi, T., Yamato, K. T., Jenkins, J., Shu, S., Ishizaki, K., Yamaoka, S., Nishihama, R., Nakamura, Y., Berger, F., et al. (2017) · Cell · doi:10.1016/j.cell.2017.09.030 · Cited by 1,205
Harke, M. J., Steffen, M. M., Gobler, C. J., Otten, T. G., Wilhelm, S. W., Wood, S. A., & Paerl, H. W. (2016) · Harmful Algae · doi:10.1016/j.hal.2015.12.007 · Cited by 1,084
Metadata
- Authors
- Krumsiek, J., Arnold, R., & Rattei, T.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2007-02-19
- Volume
- 23
- Issue
- 8
- Pages
- 1026-1028
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2165891191
- Cited by
- 718
- References
- 10
- FWCI
- 2.16
- Type
- journal article
- Language
- en
- Open access
- closed
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Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
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