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AnnotationSketch: a genome annotation drawing library

Sascha Steinbiss, Gordon Gremme, Christin Schärfer, Malte Mader, Stefan Kurtz
2008 Computer applications in the biosciences : CABIOS  
We developed a C library which provides layout and drawing capabilities for annotation features.  ...  To analyse the vast amount of genome annotation data available today, a visual representation of genomic features in a given sequence range is required.  ...  DESIGN AND IMPLEMENTATION AnnotationSketch is designed to be a small and efficient drawing library for genome annotations with a focus on simplicity, allowing to draw any given annotation in a wide variety  ... 
doi:10.1093/bioinformatics/btn657 pmid:19106120 fatcat:4rljcyck7zdklb7wexvsg4wula

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

G. J. Etherington, D. MacLean
2013 Bioinformatics  
Motivation: Drawing genomic features in attractive and informative ways is a key task in visualization of genomics data.  ...  Results: SVGenes is a Ruby-language library that uses SVG primitives to render typical genomic glyphs through a simple and flexible Ruby interface.  ...  annotation of the Arabidopsis genome  ... 
doi:10.1093/bioinformatics/btt294 pmid:23749959 pmcid:PMC3712214 fatcat:q2kfolrf2zawhegl4n5zulileq

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

Malte Mader, Ronald Simon, Sascha Steinbiss, Stefan Kurtz
2011 Journal of Clinical Bioinformatics  
Results: We have developed a web-based software FISH Oracle to visualize data from multiple array CGH experiments in a genomic context.  ...  FISH Oracle comes with a convenient data import mechanism, powerful search options for genomic elements (e.g. gene names or karyobands), quick navigation and zooming into interesting regions, and mechanisms  ...  Acknowledgements This work was supported by a grant from the Werner-Otto-Stiftung to SK and RS (# 6/73) and a grant from the Federal Ministry of Education and Research (BMBF), Germany to RS (# FKZ 01GS08189  ... 
doi:10.1186/2043-9113-1-20 pmid:21884636 pmcid:PMC3164613 fatcat:vjmj5wf6gba2vap3vpmce567t4

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

Sascha Steinbiss, Sascha Kastens, Stefan Kurtz
2012 Mobile DNA  
In two case studies, we demonstrate how LTRsift can be employed in the context of a genome-wide LTR retrotransposon survey effort.  ...  For example, about 46% of the human genome [1] and 38% of the mouse genome [2] consists of interspersed repeats, most of which are transposons.  ...  of candidates suitable for a reference library • automatic annotation of candidates with matches to a reference library • input and output of library sequences and annotations in standard output formats  ... 
doi:10.1186/1759-8753-3-18 pmid:23131050 pmcid:PMC3582472 fatcat:gza6vdbd4vgnzluazrwh7fgs7u

ParsEval: parallel comparison and analysis of gene structure annotations

Daniel S Standage, Volker P Brendel
2012 BMC Bioinformatics  
Accurate gene structure annotation is a fundamental but somewhat elusive goal of genome projects, as witnessed by the fact that (model) genomes typically undergo several cycles of re-annotation.  ...  The source code is freely available (under an ISC license) at Abstract Background: Accurate gene structure annotation is a fundamental but somewhat elusive goal of genome projects, as witnessed by the  ...  Acknowledgements The authors would like to thank the developers of the GenomeTools software for helpful feedback regarding integration of AnnotationSketch and our colleagues Drs.  ... 
doi:10.1186/1471-2105-13-187 pmid:22852583 pmcid:PMC3439248 fatcat:ufm77ghg3fh63ny66pidtzrwmi

CASSys: an integrated software-system for the interactive analysis of ChIP-seq data

Malik Alawi, Stefan Kurtz, Michael Beckstette
2011 Journal of Integrative Bioinformatics  
Chromatin-immunoprecipitation followed bymassively parallel sequencing (ChIP-seq) has become the standard technique for analyzing these interactions on a genome-wide scale.  ...  CASSys provides functionality ranging from quality assessment and -control of short reads, over the mapping of reads against a reference genome (readmapping) and the detection of enriched regions (peakdetection  ...  For a screenshot of CASSys' integrated genome browser, which makes use of the genome annotation drawing library AnnotationSketch [30] , see Figure 4 .  ... 
doi:10.1515/jib-2011-155 fatcat:sr4v2wa33fan3e4y4plm4wbuea

CASSys: an integrated software-system for the interactive analysis of ChIP-seq data

Malik Alawi, Stefan Kurtz, Michael Beckstette
2011 Journal of Integrative Bioinformatics  
Chromatin-immunoprecipitation followed by massively parallel sequencing (ChIP-seq) has become the standard technique for analyzing these interactions on a genome-wide scale.  ...  CASSys provides functionality ranging from quality assessment and -control of short reads, over the mapping of reads against a reference genome (readmapping) and the detection of enriched regions (peakdetection  ...  For a screenshot of CASSys' integrated genome browser, which makes use of the genome annotation drawing library AnnotationSketch [30] , see Figure 4 .  ... 
doi:10.2390/biecoll-jib-2011-155 pmid:21690655 fatcat:biprq2v4kfg2zhmkqgndiwnnsm

Efforts Towards Accessible And Reliable Bioinformatics

Matúš Kalaš, Inge Jonassen
2015 Zenodo  
, that is expressive enough to be usable as a common, canonical data model that serves tools, libraries, and users with convenient data interoperability.  ...  bioinformatics scenario, our work focussed in particular on the following: In the BioXSD project, we aimed at developing an XML-Schema-based data format compatible with Web services and programmatic libraries  ...  A couple of example graphics libraries for drawing genomic data are GenomeDiagram integrated in Biopython (Pritchard et al. 2006) ; AnnotationSketch, a C library within GenomeTools, with Lua, Python,  ... 
doi:10.5281/zenodo.33715 fatcat:2pxqpqu5yvat3ctdedqam3sjsi