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References

References 3.4 KB
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  1. GenomeTools publication
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  2. G. Gremme, S. Steinbiss and S. Kurtz.
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  3. GenomeTools: a comprehensive software library for efficient processing of structured genome annotations.
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  4. IEEE/ACM Transactions on Computational Biology and Bioinformatics 2013, in press.
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  5. Published software in GenomeTools
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  6. 

  7. The GenomeTools distribution includes several published software tools:
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  9.     ltrharvest, an efficient and flexible software tool for de novo detection of LTR retrotransposons.
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  10.     D. Ellinghaus, S. Kurtz, and U. Willhoeft.
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  11.     LTRharvest, a efficient and flexible software for de novo detection of LTR retrotransposons.
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  12.     BMC Bioinformatics 2008, 9:18
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  13.     tallymer, a collection of flexible and memory-efficient programs for k-mer counting and indexing of large sequence sets.
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  14.     S. Kurtz, A. Narechania, J.C. Stein, and D. Ware.
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  15.     A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes.
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  16.     BMC Genomics 2008, 9:517
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  17.     uniquesub, a program for computing minimum unique substrings.
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  18.     S. Gräf, F.G.G. Nielsen, S. Kurtz, M.A. Huynen, E. Birney, H. Stunnenberg, and P. Flicek.
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  19.     Optimized design and assessment of whole genome tiling arrays.
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  20.     Bioinformatics 2007, 23(13):i195–i204
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  21.     AnnotationSketch, a library for drawing genome annotations.
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  22.     S. Steinbiss, G. Gremme, C. Schärfer, M. Mader and S. Kurtz.
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  23.     AnnotationSketch: a genome annotation drawing library.
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  24.     Bioinformatics 2009, 25(4):533–534
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  25.     ltrdigest, a software tool for automated annotation of internal features of LTR retrotransposons.
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  26.     S. Steinbiss, U. Willhoeft, G. Gremme and S. Kurtz.
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  27.     Fine-grained annotation and classification of de novo predicted LTR retrotransposons.
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  28.     Nucleic Acids Research 2009, 37(21):7002–7013
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  29.     MetaGenomeThreader, a software to predict genes, such as PCS's (predicted coding sequences) in sequences of metagenome projects.
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  30.     D.J. Schmitz-Hübsch and S. Kurtz.
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  31.     MetaGenomeThreader: A software tool for predicting genes in DNA-sequences of metagenome projects.
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  32.     In R. Daniel and W. Streit (Eds.), Metagenomics. Methods in Molecular Biology, 325–338, Humana Press, Totowa, NJ, ISBN 978-1-60761-822-5
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  33.     GtEncseq, a compressed biosequence representation with many features.
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  34.     S. Steinbiss and S. Kurtz.
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  35.     A New Efficient Data Structure for Storage and Retrieval of Multiple Biosequences.
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  36.     IEEE/ACM Transactions on Computational Biology and Bioinformatics 2012, 9(2):345–357
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  37.     Readjoiner, a sequence assembler based on the assembly string graph framework.
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  38.     G. Gonnella and S. Kurtz.
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  39.     Readjoiner: a fast and memory efficient string graph-based sequence assembler.
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  40.     BMC Bioinformatics 2012, 13:82
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  41. 

  42. The following software tools are based on the GenomeTools library:
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  43. 

  44.     FISH Oracle, a web server for visualizing cancer genomics data.
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  45.     M. Mader, R. Simon, S. Steinbiss and S. Kurtz.
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  46.     FISH Oracle: a web server for flexible visualization of DNA copy number data in a genomic context.
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  47.     Journal of Clinical Bioinformatics 2011, 1:20
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  48.     ParsEval, a tool for comparing genome annotations.
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  49.     D.S. Standage and V.P. Brendel.
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  50.     ParsEval: parallel comparison and analysis of gene structure annotations.
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  51.     BMC Bioinformatics 2012, 13:187
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  52.     LTRsift, a graphical interface for working with LTR retrotransposon predictions.
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  53.     S. Steinbiss, S. Kastens and S. Kurtz.
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  54.     LTRsift: a graphical user interface for semi-automatic classification and postprocessing of de novo detected LTR retrotransposons.
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  55.     Mobile DNA 2012, 3:18
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  56.