Literature DB >> 19106120

AnnotationSketch: a genome annotation drawing library.

Sascha Steinbiss1, Gordon Gremme, Christin Schärfer, Malte Mader, Stefan Kurtz.   

Abstract

SUMMARY: To analyse the vast amount of genome annotation data available today, a visual representation of genomic features in a given sequence range is required. We developed a C library which provides layout and drawing capabilities for annotation features. It supports several common input and output formats and can easily be integrated into custom C applications. To exemplify the use of AnnotationSketch in other languages, we provide bindings to the scripting languages Ruby, Python and Lua. AVAILABILITY: The software is available under an open-source license as part of GenomeTools (http://genometools.org/annotationsketch.html).

Mesh:

Year:  2008        PMID: 19106120     DOI: 10.1093/bioinformatics/btn657

Source DB:  PubMed          Journal:  Bioinformatics        ISSN: 1367-4803            Impact factor:   6.937


  16 in total

1.  Sequencing the genomic regions flanking S-linked PvGLO sequences confirms the presence of two GLO loci, one of which lies adjacent to the style-length determinant gene CYP734A50.

Authors:  Benjamin A Burrows; Andrew G McCubbin
Journal:  Plant Reprod       Date:  2017-02-22       Impact factor: 3.767

2.  mtDNA Variation and Analysis Using Mitomap and Mitomaster.

Authors:  Marie T Lott; Jeremy N Leipzig; Olga Derbeneva; H Michael Xie; Dimitra Chalkia; Mahdi Sarmady; Vincent Procaccio; Douglas C Wallace
Journal:  Curr Protoc Bioinformatics       Date:  2013-12

3.  FISH Oracle: a web server for flexible visualization of DNA copy number data in a genomic context.

Authors:  Malte Mader; Ronald Simon; Sascha Steinbiss; Stefan Kurtz
Journal:  J Clin Bioinforma       Date:  2011-07-28

4.  Sequencing, annotation, and comparative genome analysis of the gerbil-adapted Helicobacter pylori strain B8.

Authors:  Max Farnbacher; Thomas Jahns; Dirk Willrodt; Rolf Daniel; Rainer Haas; Alexander Goesmann; Stefan Kurtz; Gabriele Rieder
Journal:  BMC Genomics       Date:  2010-05-27       Impact factor: 3.969

5.  SVGenes: a library for rendering genomic features in scalable vector graphic format.

Authors:  Graham J Etherington; Daniel MacLean
Journal:  Bioinformatics       Date:  2013-06-06       Impact factor: 6.937

6.  Fine-grained annotation and classification of de novo predicted LTR retrotransposons.

Authors:  Sascha Steinbiss; Ute Willhoeft; Gordon Gremme; Stefan Kurtz
Journal:  Nucleic Acids Res       Date:  2009-11       Impact factor: 16.971

7.  Molecular cloning of doublesex genes of four cladocera (water flea) species.

Authors:  Kenji Toyota; Yasuhiko Kato; Masaru Sato; Naomi Sugiura; Shinichi Miyagawa; Hitoshi Miyakawa; Hajime Watanabe; Shigeto Oda; Yukiko Ogino; Chizue Hiruta; Takeshi Mizutani; Norihisa Tatarazako; Susanne Paland; Craig Jackson; John K Colbourne; Taisen Iguchi
Journal:  BMC Genomics       Date:  2013-04-10       Impact factor: 3.969

8.  LTRsift: a graphical user interface for semi-automatic classification and postprocessing of de novo detected LTR retrotransposons.

Authors:  Sascha Steinbiss; Sascha Kastens; Stefan Kurtz
Journal:  Mob DNA       Date:  2012-11-07

9.  Transposable elements reveal a stem cell-specific class of long noncoding RNAs.

Authors:  David Kelley; John Rinn
Journal:  Genome Biol       Date:  2012-11-26       Impact factor: 13.583

10.  ParsEval: parallel comparison and analysis of gene structure annotations.

Authors:  Daniel S Standage; Volker P Brendel
Journal:  BMC Bioinformatics       Date:  2012-08-01       Impact factor: 3.169

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