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diff --git a/academic/genometools/References b/academic/genometools/References new file mode 100644 index 0000000000..b091778a4b --- /dev/null +++ b/academic/genometools/References @@ -0,0 +1,55 @@ +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 |