mirror of
https://github.com/Ponce/slackbuilds
synced 2024-11-21 19:42:24 +01:00
55 lines
3.4 KiB
Text
55 lines
3.4 KiB
Text
GenomeTools publication
|
||
G. Gremme, S. Steinbiss and S. Kurtz.
|
||
GenomeTools: a comprehensive software library for efficient processing of structured genome annotations.
|
||
IEEE/ACM Transactions on Computational Biology and Bioinformatics 2013, in press.
|
||
Published software in GenomeTools
|
||
|
||
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, 37(21):7002–7013
|
||
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, 325–338, Humana Press, Totowa, NJ, ISBN 978-1-60761-822-5
|
||
GtEncseq, a compressed biosequence representation with many features.
|
||
S. Steinbiss and S. Kurtz.
|
||
A New Efficient Data Structure for Storage and Retrieval of Multiple Biosequences.
|
||
IEEE/ACM Transactions on Computational Biology and Bioinformatics 2012, 9(2):345–357
|
||
Readjoiner, a sequence assembler based on the assembly string graph framework.
|
||
G. Gonnella and S. Kurtz.
|
||
Readjoiner: a fast and memory efficient string graph-based sequence assembler.
|
||
BMC Bioinformatics 2012, 13:82
|
||
|
||
The following software tools are based on the GenomeTools library:
|
||
|
||
FISH Oracle, a web server for visualizing cancer genomics data.
|
||
M. Mader, R. Simon, S. Steinbiss and S. Kurtz.
|
||
FISH Oracle: a web server for flexible visualization of DNA copy number data in a genomic context.
|
||
Journal of Clinical Bioinformatics 2011, 1:20
|
||
ParsEval, a tool for comparing genome annotations.
|
||
D.S. Standage and V.P. Brendel.
|
||
ParsEval: parallel comparison and analysis of gene structure annotations.
|
||
BMC Bioinformatics 2012, 13:187
|
||
LTRsift, a graphical interface for working with LTR retrotransposon predictions.
|
||
S. Steinbiss, S. Kastens and S. Kurtz.
|
||
LTRsift: a graphical user interface for semi-automatic classification and postprocessing of de novo detected LTR retrotransposons.
|
||
Mobile DNA 2012, 3:18
|