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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  
Hence they are well suited for computational identification. Current software allows for a comprehensive genome-wide de novo detection of such elements.  ...  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  ...  Acknowledgements The authors wish to thank Gordon Gremme for the GenomeTools software, without which the development of LTRsift would not have been possible.  ... 
doi:10.1186/1759-8753-3-18 pmid:23131050 pmcid:PMC3582472 fatcat:gza6vdbd4vgnzluazrwh7fgs7u

Visual programming for next-generation sequencing data analytics

Franco Milicchio, Rebecca Rose, Jiang Bian, Jae Min, Mattia Prosperi
2016 BioData Mining  
Here we scrutinize the state-of-the-art low-level software libraries implemented specifically for NGS and graphical tools for NGS analytics.  ...  Although a plethora of tools for NGS data analysis has emerged in the past decade, (i) software development is still lagging behind data generation capabilities, and (ii) there is a 'cultural' gap between  ...  Table 1 gives a description of the most popular libraries and toolsets for sequence analysis and NGS data processing.  ... 
doi:10.1186/s13040-016-0095-3 pmid:27127540 pmcid:PMC4848821 fatcat:tvbjlx36hbgblb5x5dl7tah6fe

ParsEval: parallel comparison and analysis of gene structure annotations

Daniel S Standage, Volker P Brendel
2012 BMC Bioinformatics  
We developed ParsEval, a software application for pairwise comparison of sets of gene structure annotations.  ...  We developed ParsEval, a software application for pairwise comparison of sets of gene structure annotations.  ...  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

Leveraging multiple transcriptome assembly methods for improved gene structure annotation [article]

Luca Venturini, Shabhonam Caim, Gemy Kaithakottil, Daniel Lee Mapleson, David Swarbreck
2017 bioRxiv   pre-print
annotation.  ...  Here we show that the accuracy of transcript reconstruction can be boosted by combining multiple approaches, and we present a novel algorithm to integrate multiple RNA-Seq assemblies into a coherent transcript  ...  Acknowledgements This research was supported in part by the NBI Computing infrastructure for Science (CiS) group.  ... 
doi:10.1101/216994 fatcat:uw7ymsrgjfanbkoqs5olqnwnhq

LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons

David Ellinghaus, Stefan Kurtz, Ute Willhoeft
2008 BMC Bioinformatics  
Conclusion: LTRharvest is an efficient software tool delivering high quality annotation of LTR retrotransposons.  ...  It can, for example, process the largest human chromosome in approx. 8 minutes on a Linux PC with 4 GB of memory.  ...  We thank A. Kalyanaraman for sending a copy of his LTR_seq program and Z. Xu for sending a copy of the LTR_FINDER program.  ... 
doi:10.1186/1471-2105-9-18 pmid:18194517 pmcid:PMC2253517 fatcat:wvexkjstjzd4vma4lybnz3blpe

Efforts Towards Accessible And Reliable Bioinformatics

Matúš Kalaš, Inge Jonassen
2015 Zenodo  
The eSysbio project explored ways of developing a workbench for collaborative data analysis, accessible in various ways for users with various tasks and expertise.  ...  The aim of the presented work was contributing to making scientific computing more accessible, reliable, and thus more efficient for researchers, primarily computational biologists and molecular biologists  ...  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

FISH Oracle 2: a web server for integrative visualization of genomic data in cancer research

Malte Mader, Ronald Simon, Stefan Kurtz
2014 Journal of Clinical Bioinformatics  
A comprehensive view on all relevant genomic data is instrumental for understanding the complex patterns of molecular alterations typically found in cancer cells.  ...  Results: We developed FISH Oracle 2, a web server for the interactive visualization of different kinds of downstream processed genomics data typically available in cancer research.  ...  Acknowledgements This work was supported by a grant from the Monika-Kutzner-Stiftung to SK. We thank Ole Eigenbrod for performing the analysis of SNP and expression data.  ... 
doi:10.1186/2043-9113-4-5 pmid:24684958 pmcid:PMC4230720 fatcat:zc7pwesthngshlqwit6ejh3qea

High-quality genome assembly of the soybean fungal pathogen Cercospora kikuchii

Takeshi Kashiwa, Tomohiro Suzuki
2021 G3: Genes, Genomes, Genetics  
Here, we report for the first time, a chromosome-level genome assembly for C. kikuchii. The genome assembly of 9 contigs was 34.44 Mb and the N50 was 4.19 Mb.  ...  Plant diseases caused by the Cercospora genus of ascomycete fungi are a major concern for commercial agricultural practices.  ...  Kurtz, 2013 GenomeTools: A comprehensive 337 software library for efficient processing of structured genome annotations. IEEE/ACM 338 Trans. Comput. Biol.  ... 
doi:10.1093/g3journal/jkab277 pmid:34568928 pmcid:PMC8496228 fatcat:czg4t2zxorbodlap4m4nky7kx4

LTR_retriever: A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons

Shujun Ou, Ning Jiang
2017 Plant Physiology  
Long terminal repeat retrotransposons (LTR-RTs) are prevalent in plant genomes. The identification of LTR-RTs is critical for achieving high-quality gene annotation.  ...  Here, we report LTR_retriever, a multithreading-empowered Perl program that identifies LTR-RTs and generates high-quality LTR libraries from genomic sequences.  ...  Yi Liao (Institute of Genetics and Developmental Biology, Chinese Academy of Sciences) for valuable discussions. We thank Stefan Cerbin and Drs.  ... 
doi:10.1104/pp.17.01310 pmid:29233850 pmcid:PMC5813529 fatcat:kmlxq45dajfk7bxsbc2nr5ewyi

SMRT sequencing generates the chromosome-scale reference genome of tropical fruit mango, Mangifera indica [article]

Wei Li, Xun-Ge Zhu, Qun-Jie Zhang, Kui Li, Dan Zhang, Cong Shi, Li-Zhi Gao
2020 bioRxiv   pre-print
Mango (Mangifera indica), a member of the family Anacardiaceae, is one of the world's most popular tropical fruits.  ...  Aided with the published genetic map, for the first time, we assembled the M. indica genome to the chromosomes, and finally about 98.77% of the genome assembly was anchored to 20 pseudo-chromosomes.  ...  Acknowledgements This work was supported by Yunnan Innovation Team Project and Natural Science Foundation of Yunnan (to L.-Z.G.).  ... 
doi:10.1101/2020.02.22.960880 fatcat:f6a5xzpnjrf3ho5kteel4elztq

Universal correction of enzymatic sequence bias reveals molecular signatures of protein/DNA interactions

André L Martins, Ninad M Walavalkar, Warren D Anderson, Chongzhi Zang, Michael J Guertin
2017 Nucleic Acids Research  
Molecular genomics techniques are continually refined to provide higher resolution mapping of nucleic acid interactions and structure.  ...  Enzymatic sequence biases are most well-characterized for DNase-seq experiments (10-12), but nearly all molecular genomics experiments employ enzymatic treatments and these enzymes also have intrinsic  ...  The C library and the corresponding header files are built as part of the main compilation process and can be linked as typical for C libraries.  ... 
doi:10.1093/nar/gkx1053 pmid:29126307 pmcid:PMC5778497 fatcat:ci2nlk4scrbphc43hzxrp2vfae

Long-Read Annotation: Automated Eukaryotic Genome Annotation Based on Long-Read cDNA Sequencing

David E. Cook, Jose Espejo Valle-Inclan, Alice Pajoro, Hanna Rovenich, Bart P.H.J. Thomma, Luigi Faino
2018 Plant Physiology  
Based on annotations of two fungal genomes (Verticillium dahliae and Plicaturopsis crispa) and two plant genomes (Arabidopsis [Arabidopsis thaliana] and Oryza sativa), we show that LoReAn outperforms popular  ...  genome annotations.  ...  ACKNOWLEDGMENTS We thank Jordi Coolen for his assistance in writing the LoReAn software and Michael Seidl for reading the manuscript.  ... 
doi:10.1104/pp.18.00848 pmid:30401722 pmcid:PMC6324239 fatcat:txf5xlfopzevbnfbprimscezni

Plant-RRBS, a bisulfite and next-generation sequencing-based methylome profiling method enriching for coverage of cytosine positions

Martin Schmidt, Michiel Van Bel, Magdalena Woloszynska, Bram Slabbinck, Cindy Martens, Marc De Block, Frederik Coppens, Mieke Van Lijsebettens
2017 BMC Plant Biology  
Cytosine methylation in plant genomes is important for the regulation of gene transcription and transposon activity.  ...  Plant-RRBS reproducibly covers commonly up to one fourth of the cytosine positions in the rice genome when using MspI-DpnII within a group of five biological replicates of a line.  ...  Annick Bleys for the critical reading of the manuscript and the precious help to improve and finalize it.  ... 
doi:10.1186/s12870-017-1070-y pmid:28683715 pmcid:PMC5501559 fatcat:ummg2nyw55eilp2ywpxbpg6eui

Genomics as a service: A joint computing and networking perspective

G. Reali, M. Femminella, E. Nunzi, D. Valocchi
2018 Computer Networks  
This paper provides a global picture about the deployment of networked processing services for genomic data sets.  ...  , but also the main software technologies available to develop genomic processing services.  ...  GenomeTools [179] is a software library designed for developing bioinformatics software intended to create, process or convert annotation graphs.  ... 
doi:10.1016/j.comnet.2018.08.005 fatcat:w562rwbavnax7pbtairhtnadje

Interpreting functional effects of coding variants: challenges in proteome-scale prediction, annotation and assessment

Khader Shameer, Lokesh P. Tripathi, Krishna R. Kalari, Joel T. Dudley, Ramanathan Sowdhamini
2015 Briefings in Bioinformatics  
Dr Sowdhamini developed and improved on a wide range of computational methods, prediction algorithms, open-access web servers, publicly databases and software systems for the analysis of genomes and proteomes  ...  In this review, we provide an overview of the bioinformatics resources for the prediction, annotation and visualization of coding single nucleotide variants.  ...  Acknowledgements K.S. and J.T.D would like to thank Icahn Institute for Genomics and Multiscale Biology (http://icahn.mssm.edu/ departments-and-institutes/genomics), Mount Sinai Health System for infrastructural  ... 
doi:10.1093/bib/bbv084 pmid:26494363 pmcid:PMC6078163 fatcat:xeldhpluhjajnnatu44secmb3u
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