Difference between revisions of "GenomeTools"
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{{Bioinformatics application | {{Bioinformatics application | ||
|sw summary=The GenomeTools genome analysis system is a free collection of bioinformatics tools for genome informatics. | |sw summary=The GenomeTools genome analysis system is a free collection of bioinformatics tools for genome informatics. | ||
| − | |bio domain=Genomics, | + | |bio domain=Genomics, |
| − | |created by=Gremme G, Kurtz S, | + | |created by=Gremme G, Kurtz S, |
| − | |sw feature=Integrated solution, | + | |sw feature=Integrated solution, |
| − | |language=C, | + | |language=C, |
| − | |licence=BSD, | + | |licence=BSD, |
|os=POSIX, Unix, Linux, Mac OS X, OpenBSD, Windows (Cygwin) | |os=POSIX, Unix, Linux, Mac OS X, OpenBSD, Windows (Cygwin) | ||
}} | }} | ||
| − | + | The GenomeTools distribution includes several published software tools: | |
| − | + | * ltrharvest, an efficient and flexible software tool for de novo detection of LTR retrotransposons. | |
| − | + | D. Ellinghaus, S. Kurtz, and U. Willhoeft. | |
| − | + | LTRharvest, a efficient and flexible software for de novo detection of LTR retrotransposons. | |
| − | + | BMC Bioinformatics 2008, 9:18 | |
| − | + | * tallymer, a collection of flexible and memory-efficient programs for k-mer counting and indexing of large sequence sets. | |
| − | + | S. Kurtz, A. Narechania, J.C. Stein, and D. Ware. | |
| − | + | A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes. | |
| − | + | BMC Genomics 2008, 9:517 | |
| − | + | * uniquesub, a program for computing minimum unique substrings. | |
| − | + | S. Gräf, F.G.G. Nielsen, S. Kurtz, M.A. Huynen, E. Birney, H. Stunnenberg, and P. Flicek. | |
| − | + | Optimized design and assessment of whole genome tiling arrays. | |
| − | + | Bioinformatics 2007, 23(13):i195–i204 | |
| − | + | * AnnotationSketch, a library for drawing genome annotations. | |
| − | + | S. Steinbiss, G. Gremme, C. Schärfer, M. Mader and S. Kurtz. | |
| − | + | AnnotationSketch: a genome annotation drawing library. | |
| − | + | Bioinformatics 2009, 25(4):533–534 | |
| − | + | * ltrdigest, a software tool for automated annotation of internal features of LTR retrotransposons. | |
| − | + | S. Steinbiss, U. Willhoeft, G. Gremme and S. Kurtz. | |
| − | + | Fine-grained annotation and classification of de novo predicted LTR retrotransposons. | |
| − | + | Nucleic Acids Research 2009, doi: 10.1093/nar/gkp759 | |
| − | + | * MetaGenomeThreader, a software to predict genes, such as PCS's (predicted coding sequences) in sequences of metagenome projects. | |
| − | + | D.J. Schmitz-Hübsch and S. Kurtz. | |
| − | + | MetaGenomeThreader: A software tool for predicting genes in DNA-sequences of metagenome projects. | |
| − | + | In R. Daniel and W. Streit (Eds.), Metagenomics. Methods in Molecular Biology, Humana Press, Totowa, NJ, in press | |
Revision as of 20:30, 10 May 2010
|
Application data |
|
| Created by | Gremme G, Kurtz S |
|---|---|
| Biological application domain(s) | Genomics |
| Maintained? | Maybe |
| Software features | Integrated solution |
| Programming language(s) | C |
| Licence | BSD |
| Operating system(s) | POSIX, Unix, Linux, Mac OS X, OpenBSD, Windows (Cygwin) |
Summary: The GenomeTools genome analysis system is a free collection of bioinformatics tools for genome informatics.
"Error: no local variable "counter" was set." is not a number.
The GenomeTools distribution includes several published software tools:
- ltrharvest, an efficient and flexible software tool for de novo detection of LTR retrotransposons.
D. Ellinghaus, S. Kurtz, and U. Willhoeft. LTRharvest, a efficient and flexible software for de novo detection of LTR retrotransposons. BMC Bioinformatics 2008, 9:18
- tallymer, a collection of flexible and memory-efficient programs for k-mer counting and indexing of large sequence sets.
S. Kurtz, A. Narechania, J.C. Stein, and D. Ware. A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes. BMC Genomics 2008, 9:517
- uniquesub, a program for computing minimum unique substrings.
S. Gräf, F.G.G. Nielsen, S. Kurtz, M.A. Huynen, E. Birney, H. Stunnenberg, and P. Flicek. Optimized design and assessment of whole genome tiling arrays. Bioinformatics 2007, 23(13):i195–i204
- AnnotationSketch, a library for drawing genome annotations.
S. Steinbiss, G. Gremme, C. Schärfer, M. Mader and S. Kurtz. AnnotationSketch: a genome annotation drawing library. Bioinformatics 2009, 25(4):533–534
- ltrdigest, a software tool for automated annotation of internal features of LTR retrotransposons.
S. Steinbiss, U. Willhoeft, G. Gremme and S. Kurtz. Fine-grained annotation and classification of de novo predicted LTR retrotransposons. Nucleic Acids Research 2009, doi: 10.1093/nar/gkp759
- MetaGenomeThreader, a software to predict genes, such as PCS's (predicted coding sequences) in sequences of metagenome projects.
D.J. Schmitz-Hübsch and S. Kurtz. MetaGenomeThreader: A software tool for predicting genes in DNA-sequences of metagenome projects. In R. Daniel and W. Streit (Eds.), Metagenomics. Methods in Molecular Biology, Humana Press, Totowa, NJ, in press
