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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  
Long terminal repeat (LTR) retrotransposons are a class of eukaryotic mobile elements characterized by a distinctive sequence similarity-based structure. Hence they are well suited for computational identification. Current software allows for a comprehensive genome-wide de novo detection of such elements. The obvious next step is the classification of newly detected candidates resulting in (super-)families. Such a de novo classification approach based on sequence-based clustering of transposon
more » ... ring of transposon features has been proposed before, resulting in a preliminary assignment of candidates to families as a basis for subsequent manual refinement. However, such a classification workflow is typically split across a heterogeneous set of glue scripts and generic software (for example, spreadsheets), making it tedious for a human expert to inspect, curate and export the putative families produced by the workflow. Results: We have developed LTRsift , an interactive graphical software tool for semi-automatic postprocessing of de novo predicted LTR retrotransposon annotations. Its user-friendly interface offers customizable filtering and classification functionality, displaying the putative candidate groups, their members and their internal structure in a hierarchical fashion. To ease manual work, it also supports graphical user interface-driven reassignment, splitting and further annotation of candidates. Export of grouped candidate sets in standard formats is possible. In two case studies, we demonstrate how LTRsift can be employed in the context of a genome-wide LTR retrotransposon survey effort. Conclusions: LTRsift is a useful and convenient tool for semi-automated classification of newly detected LTR retrotransposons based on their internal features. Its efficient implementation allows for convenient and seamless filtering and classification in an integrated environment. Developed for life scientists, it is helpful in postprocessing and refining the output of software for predicting LTR retrotransposons up to the stage of preparing full-length reference sequence libraries. The LTRsift software is freely available at http://www.zbh.uni-hamburg.de/LTRsift under an open-source license. in the genomes of many higher organisms. 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. These, in turn, are further characterized by their transposition mechanism: class I transposons or retrotransposons replicate via an RNA intermediate, while class II transposons or DNA transposons replicate via a DNA intermediate [3, 4] . An important order of retrotransposons are LTR retrotransposons, which are less common in animals, but the predominant order in plants. Similar in structure to retroviruses (Figure 1 ), they show long terminal repeat
doi:10.1186/1759-8753-3-18 pmid:23131050 pmcid:PMC3582472 fatcat:gza6vdbd4vgnzluazrwh7fgs7u

AnnotationSketch: a genome annotation drawing library

Sascha Steinbiss, Gordon Gremme, Christin Schärfer, Malte Mader, Stefan Kurtz
2008 Computer applications in the biosciences : CABIOS  
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.
more » ... and Lua. Availability: The software is available under an open-source license as part of GenomeTools (http://genometools.org/annotationsketch. html).
doi:10.1093/bioinformatics/btn657 pmid:19106120 fatcat:4rljcyck7zdklb7wexvsg4wula

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

Sascha Steinbiss, Ute Willhoeft, Gordon Gremme, Stefan Kurtz
2009 Nucleic Acids Research  
Tel: +49 40 42838 7322; Fax: +49 40 42838 7312; Email: steinbiss@zbh.uni-hamburg.de ( Figure 1A ).  ... 
doi:10.1093/nar/gkp759 pmid:19786494 pmcid:PMC2790888 fatcat:26zke6pvaveirdkjvdcc2zxv7m

GFF3toEMBL: Preparing annotated assemblies for submission to EMBL

Andrew J. Page, Sascha Steinbiss, Ben Taylor, Torsten Seemann, Jacqueline A. Keane
2016 Journal of Open Source Software  
Built on the Genome-Tools annotation processing library (Gremme, Steinbiss, and Kurtz 2013) , GFF3toEMBL is robust, fast, memory efficient and well tested, and has been used to submit more than 30% of  ... 
doi:10.21105/joss.00080 fatcat:qyudkhjstvh47f2dxmewr7ygqm

Companion: a web server for annotation and analysis of parasite genomes

Sascha Steinbiss, Fatima Silva-Franco, Brian Brunk, Bernardo Foth, Christiane Hertz-Fowler, Matthew Berriman, Thomas D. Otto
2016 Nucleic Acids Research  
Currently available sequencing technologies enable quick and economical sequencing of many new eukaryotic parasite (apicomplexan or kinetoplastid) species or strains. Compared to SNP calling approaches, de novo assembly of these genomes enables researchers to additionally determine insertion, deletion and recombination events as well as to detect complex sequence diversity, such as that seen in variable multigene families. However, there currently are no automated eukaryotic annotation
more » ... annotation pipelines offering the required range of results to facilitate such analyses. A suitable pipeline needs to perform evidence-supported gene finding as well as functional annotation and pseudogene detection up to the generation of output ready to be submitted to a public database. Moreover, no current tool includes quick yet informative comparative analyses and a first pass visualization of both annotation and analysis results. To overcome those needs we have developed the Companion web server (http://companion. sanger.ac.uk) providing parasite genome annotation as a service using a reference-based approach. We demonstrate the use and performance of Companion by annotating two Leishmania and Plasmodium genomes as typical parasite cases and evaluate the results compared to manually annotated references.
doi:10.1093/nar/gkw292 pmid:27105845 pmcid:PMC4987884 fatcat:p4oulubu4zcltnnaipaaedk52u

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  
The rapidly growing amount of array CGH data requires improved visualization software supporting the process of identifying candidate cancer genes. Optimally, such software should work across multiple microarray platforms, should be able to cope with data from different sources and should be easy to operate. Results: We have developed a web-based software FISH Oracle to visualize data from multiple array CGH experiments in a genomic context. Its fast visualization engine and advanced web and
more » ... advanced web and database technology supports highly interactive use. 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 to export the visualization into different high quality formats. These features make the software especially suitable for the needs of life scientists. Conclusions: FISH Oracle offers a fast and easy to use visualization tool for array CGH and SNP array data. It allows for the identification of genomic regions representing minimal common changes based on data from one or more experiments. FISH Oracle will be instrumental to identify candidate onco and tumor suppressor genes based on the frequency and genomic position of DNA copy number changes. The FISH Oracle application and an installed demo web server are available at
doi:10.1186/2043-9113-1-20 pmid:21884636 pmcid:PMC3164613 fatcat:vjmj5wf6gba2vap3vpmce567t4

First Draft Genome Sequence of the Dourine Causative Agent: Trypanosoma Equiperdum Strain OVI

Laurent Hébert, Bouziane Moumen, Anthony Madeline, Sascha Steinbiss, Latifa Lakhdar, Nick Van Reet, Philippe Büscher, Claire Laugier, Julien Cauchard, Sandrine Petry
2017 Journal of Genomics  
Trypanosoma equiperdum is the causative agent of dourine, a sexually-transmitted infection of horses. This parasite belongs to the subgenus Trypanozoon that also includes the agent of sleeping sickness (Trypanosoma brucei) and surra (Trypanosoma evansi). We herein report the genome sequence of a T. equiperdum strain OVI, isolated from a horse in South-Africa in 1976. This is the first genome sequence of the T. equiperdum species, and its availability will provide important insights for future
more » ... sights for future studies on genetic classification of the subgenus Trypanozoon.
doi:10.7150/jgen.17904 pmid:28138343 pmcid:PMC5278650 fatcat:k7aakizxnjdp7hlfsvvavfvzhm

An expressed, endogenous Nodavirus-like element captured by a retrotransposon in the genome of the plant parasitic nematode Bursaphelenchus xylophilus

James A. Cotton, Sascha Steinbiss, Toshiro Yokoi, Isheng J. Tsai, Taisei Kikuchi
2016 Scientific Reports  
Cotton 1 ,"Sascha"Steinbiss 1 ,"Toshiro"Yokoi 2 ,"Isheng"J."  ... 
doi:10.1038/srep39749 pmid:28004836 pmcid:PMC5177903 fatcat:kkvvz5espnemjk37a4lpd7ys44

Genome organization and DNA accessibility control antigenic variation in trypanosomes

Laura S. M. Müller, Raúl O. Cosentino, Konrad U. Förstner, Julien Guizetti, Carolin Wedel, Noam Kaplan, Christian J. Janzen, Panagiota Arampatzi, Jörg Vogel, Sascha Steinbiss, Thomas D. Otto, Antoine-Emmanuel Saliba (+2 others)
2018 Nature  
Many evolutionarily distant pathogenic organisms have evolved similar survival strategies to evade the immune responses of their hosts. These include antigenic variation, through which an infecting organism prevents clearance by periodically altering the identity of proteins that are visible to the immune system of the host 1 . Antigenic variation requires large reservoirs of immunologically diverse antigen genes, which are often generated through homologous recombination, as well as mechanisms
more » ... well as mechanisms to ensure the expression of one or very few antigens at any given time. Both homologous recombination and gene expression are affected by threedimensional genome architecture and local DNA accessibility 2,3 . Factors that link three-dimensional genome architecture, local chromatin conformation and antigenic variation have, to our knowledge, not yet been identified in any organism. One of the major obstacles to studying the role of genome architecture in antigenic variation has been the highly repetitive nature and heterozygosity of antigen-gene arrays, which has precluded complete genome assembly in many pathogens. Here we report the de novo haplotypespecific assembly and scaffolding of the long antigen-gene arrays of the model protozoan parasite Trypanosoma brucei, using longread sequencing technology and conserved features of chromosome folding 4 . Genome-wide chromosome conformation capture (Hi-C) reveals a distinct partitioning of the genome, with antigen-encoding subtelomeric regions that are folded into distinct, highly compact compartments. In addition, we performed a range of analyses-Hi-C, fluorescence in situ hybridization, assays for transposaseaccessible chromatin using sequencing and single-cell RNA sequencing-that showed that deletion of the histone variants H3.V and H4.V increases antigen-gene clustering, DNA accessibility across sites of antigen expression and switching of the expressed antigen isoform, via homologous recombination. Our analyses identify histone variants as a molecular link between global genome architecture, local chromatin conformation and antigenic variation. Genome sequences of several pathogens have revealed a partitioning of chromosomes, with housekeeping genes often being located in the central core and antigen genes being located in subtelomeric regions 5,6 . These assemblies suggest that the linear organization of the genome may be important for restricting high levels of recombination to regions that code for antigens and for ensuring that all but one antigen is repressed. Recently, genome-wide Hi-C analyses have begun to uncover the 3D organization of chromosomes at high resolution 4 , which has highlighted the critical role of spatial organization and compartmentalization of DNA in the regulation of gene expression and recombination 2,3 . OPEN 1 N O V e M B e r 2 0 1 8 | V O L 5 6 3 | N A t U r e | 1 2 1 Fig. 1 | Long-read and Hi-C-based de novo assembly of the T. brucei Lister 427 genome. Only one of the two homologous chromosomes (chr.) is depicted for the homozygous chromosomal core regions (22.71 Mb). Both chromosomes are shown for the heterozygous subtelomeric regions (19.54 Mb). Relative transcript levels (window size, 5,001 bp; step size, 101 bp) are shown as a black line above each chromosome. BESs and MESs were assigned to the respective subtelomeric region if an unambiguous assignment based on DNA interaction data was possible (see Supplementary Information). Centromeres were assigned based on KKT2 ChIP-seq data 30 . 1 2 2 | N A t U r e | V O L 5 6 3 | 1 N O V e M B e r 2 0 1 8 . for critical reading of the manuscript. We thank T. Achmedov for scRNA-seq technical assistance, M. Berriman, G. Ramasamy, P. Myler and L. Barquist for assistance with the genome assembly, J. Dekker, M. Imakaev, J. M. Belton and B. R. Lajoie for advice on Hi-C experimental design and analysis, K. Ersfeld for advice on epitope tagging of SCC1 and FISH, S. Kirchner and A. R. Batista for suggestions on ATAC-seq, T. Straub and F. Goth for providing server space and all members of the Engstler, Janzen, Kramer, Morriswood and Ladurner laboratories for valuable discussions. We thank C. Clayton and L. Glover for reagents and M. Urbiniak for sharing unpublished SCC1 data.
doi:10.1038/s41586-018-0619-8 pmid:30333624 fatcat:635mhdd6zfam5adcrvg5zp5hcm

khmer release v2.1: software for biological sequence analysis

Daniel Standage, Ali yari, Lisa J. Cohen, Michael R. Crusoe, Tim Head, Luiz Irber, Shannon EK Joslin, N. B. Kingsley, Kevin D. Murray, Russell Neches, Camille Scott, Ryan Shean (+3 others)
2017 Journal of Open Source Software  
doi:10.21105/joss.00272 fatcat:dvsn2kh7rjgf7ejmar4doczwle

Complete avian malaria parasite genomes reveal features associated with lineage specific evolution in birds and mammals [article]

Ulrike Boehme, Thomas D. Otto, James Cotton, Sascha Steinbiss, Mandy Sanders, Samuel O. Oyola, Antoine Nicot, Sylvain Gandon, Kailash P. Patra, Colin Herd, Ellen Bushell, Katarzyna K. Modrzynska (+5 others)
2016 bioRxiv   pre-print
A single complete, 5.7 kb retrotransposon is present in P. gallinaceum (PGAL8A_00410600) (Fig. 3A) (Steinbiss et al. 2009 ).  ...  P. relictum did not contain a complete retrotransposon but based on the programs LTRharvest/LTRdigest (Ellinghaus et al. 2008; Steinbiss et al. 2009 ), we found 7 near full--length copies with all the  ... 
doi:10.1101/086504 fatcat:7tszeydll5awfhkso6ojv562mu

A new Plasmodium vivax reference sequence with improved assembly of the subtelomeres reveals an abundance of pir genes

Sarah Auburn, Ulrike Böhme, Sascha Steinbiss, Hidayat Trimarsanto, Jessica Hostetler, Mandy Sanders, Qi Gao, François Nosten, Chris I. Newbold, Matthew Berriman, Ric N. Price, Thomas D. Otto
2016 Wellcome Open Research  
is now the predominant cause of malaria in the Asia-Pacific, Plasmodium vivax South America and Horn of Africa. Laboratory studies of this species are constrained by the inability to maintain the parasite in continuous ex vivo culture, but genomic approaches provide an alternative and complementary avenue to investigate the parasite's biology and epidemiology.
doi:10.12688/wellcomeopenres.9876.1 pmid:28008421 pmcid:PMC5172418 fatcat:4lzalql35zahtayvg57o26a47q

Complete avian malaria parasite genomes reveal features associated with lineage-specific evolution in birds and mammals

Ulrike Böhme, Thomas D. Otto, James A. Cotton, Sascha Steinbiss, Mandy Sanders, Samuel O. Oyola, Antoine Nicot, Sylvain Gandon, Kailash P. Patra, Colin Herd, Ellen Bushell, Katarzyna K. Modrzynska (+5 others)
2018 Genome Research  
Based on the order of encoded HMM domains, the P. gallinaceum retrotransposon can be classified as Ty3/Gypsy retrotransposon (Steinbiss et al. 2009 ).  ...  P. relictum did not contain a complete retrotransposon, but based on the programs LTRharvest/LTRdigest (Ellinghaus et al. 2008; Steinbiss et al. 2009 ), we found seven near full-length copies with all  ... 
doi:10.1101/gr.218123.116 pmid:29500236 pmcid:PMC5880244 fatcat:yhonxdqcqfeozcp5ydctrktney

Community-driven development for computational biology at Sprints, Hackathons and Codefests

Steffen Möller, Enis Afgan, Michael Banck, Raoul JP Bonnal, Timothy Booth, John Chilton, Peter JA Cock, Markus Gumbel, Nomi Harris, Richard Holland, Matúš Kalaš, László Kaján (+16 others)
2014 BMC Bioinformatics  
Computational biology comprises a wide range of technologies and approaches. Multiple technologies can be combined to create more powerful workflows if the individuals contributing the data or providing tools for its interpretation can find mutual understanding and consensus. Much conversation and joint investigation are required in order to identify and implement the best approaches. Traditionally, scientific conferences feature talks presenting novel technologies or insights, followed up by
more » ... s, followed up by informal discussions during coffee breaks. In multi-institution collaborations, in order to reach agreement on implementation details or to transfer deeper insights in a technology and practical skills, a representative of one group typically visits the other. However, this does not scale well when the number of technologies or research groups is large. Conferences have responded to this issue by introducing Birds-of-a-Feather (BoF) sessions, which offer an opportunity for individuals with common interests to intensify their interaction. However, parallel BoF sessions often make it hard for participants to join multiple BoFs and find common ground between the different technologies, and BoFs are generally too short to allow time for participants to program together. Results: This report summarises our experience with computational biology Codefests, Hackathons and Sprints, which are interactive developer meetings. They are structured to reduce the limitations of traditional scientific meetings described above by strengthening the interaction among peers and letting the participants determine the schedule and topics. These meetings are commonly run as loosely scheduled "unconferences" (self-organized identification of participants and topics for meetings) over at least two days, with early introductory talks to welcome and organize contributors, followed by intensive collaborative coding sessions. We summarise some prominent achievements of those meetings and describe differences in how these are organised, how their audience is addressed, and their outreach to their respective communities. Conclusions: Hackathons, Codefests and Sprints share a stimulating atmosphere that encourages participants to jointly brainstorm and tackle problems of shared interest in a self-driven proactive environment, as well as providing an opportunity for new participants to get involved in collaborative projects.
doi:10.1186/1471-2105-15-s14-s7 pmid:25472764 pmcid:PMC4255748 fatcat:p7jbtuipnbdafo3zauaqrhu5sq

The genome of the sparganosis tapeworm Spirometra erinaceieuropaeiisolated from the biopsy of a migrating brain lesion

Hayley M Bennett, Hoi Ping Mok, Effrossyni Gkrania-Klotsas, Isheng J Tsai, Eleanor J Stanley, Nagui M Antoun, Avril Coghlan, Bhavana Harsha, Alessandra Traini, Diogo M Ribeiro, Sascha Steinbiss, Sebastian B Lucas (+8 others)
2014 Genome Biology  
Sparganosis is an infection with a larval Diphyllobothriidea tapeworm. From a rare cerebral case presented at a clinic in the UK, DNA was recovered from a biopsy sample and used to determine the causative species as Spirometra erinaceieuropaei through sequencing of the cox1 gene. From the same DNA, we have produced a draft genome, the first of its kind for this species, and used it to perform a comparative genomics analysis and to investigate known and potential tapeworm drug targets in this
more » ... targets in this tapeworm. Results: The 1.26 Gb draft genome of S. erinaceieuropaei is currently the largest reported for any flatworm. Through investigation of β-tubulin genes, we predict that S. erinaceieuropaei larvae are insensitive to the tapeworm drug albendazole. We find that many putative tapeworm drug targets are also present in S. erinaceieuropaei, allowing possible cross application of new drugs. In comparison to other sequenced tapeworm species we observe expansion of protease classes, and of Kuntiz-type protease inhibitors. Expanded gene families in this tapeworm also include those that are involved in processes that add post-translational diversity to the protein landscape, intracellular transport, transcriptional regulation and detoxification. Conclusions: The S. erinaceieuropaei genome begins to give us insight into an order of tapeworms previously uncharacterized at the genome-wide level. From a single clinical case we have begun to sketch a picture of the characteristics of these organisms. Finally, our work represents a significant technological achievement as we present a draft genome sequence of a rare tapeworm, and from a small amount of starting material.
doi:10.1186/s13059-014-0510-3 fatcat:3juuz7gfizb3xnxso3k67q37za
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