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Cinteny: flexible analysis and visualization of synteny and genome rearrangements in multiple organisms

Amit U Sinha, Jaroslaw Meller
2007 BMC Bioinformatics  
Therefore, existing tools and resources that facilitate identification, visualization and analysis of synteny need to be further improved to provide a flexible platform for such analysis, especially in  ...  In particular, Cinteny provides: i) integration of synteny browsing with assessment of evolutionary distances for multiple genomes; ii) flexibility to adjust the parameters and re-compute the results on-the-fly  ...  Acknowledgements This work has been supported by NIH grants R21 AI055338 and R01 AR050688.  ... 
doi:10.1186/1471-2105-8-82 pmid:17343765 pmcid:PMC1821339 fatcat:dddodla73bb6vplkvurs234sna

Visualizing genomes: techniques and challenges

Cydney B Nielsen, Michael Cantor, Inna Dubchak, David Gordon, Ting Wang
2010 Nature Methods  
Here we provide a guide to genomic data visualization tools that facilitate analysis tasks by enabling researchers to explore, interpret and manipulate their data, and in some cases perform on-the-fly  ...  We will discuss graphical methods designed for the analysis of de novo sequencing assemblies and read alignments, genome browsing, and comparative genomics, highlighting the strengths and limitations of  ...  in multiple genomes and over multiple scales.  ... 
doi:10.1038/nmeth.1422 pmid:20195257 fatcat:3gxjhrkvxzfzllbxk4jt4vll2m

Tasks, Techniques, and Tools for Genomic Data Visualization [article]

Sabrina Nusrat, Theresa Harbig, Nils Gehlenborg
2019 arXiv   pre-print
Furthermore, we provide a comprehensive review of published genomic visualization tools in the context of the proposed taxonomies.  ...  A key challenge in data-driven research is to discover unexpected patterns and to formulate hypotheses in an unbiased manner in vast amounts of genomic and other associated data.  ...  Acknowledgements The authors thank Peter Kerpedjiev for his contributions to the initial list of manuscripts and tools that are discussed in this survey.  ... 
arXiv:1905.02853v1 fatcat:sty44l3yzbfvjlgv626rm6wb74

OrthoCluster

Xinghuo Zeng, Matthew J. Nesbitt, Jian Pei, Ke Wang, Ismael A. Vergara, Nansheng Chen
2008 Proceedings of the 11th international conference on Extending database technology Advances in database technology - EDBT '08  
Synteny blocks, which are conserved blocks of genes on chromosomes of related species, play important roles in comparative genomics analysis.  ...  By comparing genomes among both closely and distally related species, comparative genomics analysis characterizes structures and functions of different genomes in both conserved and divergent regions.  ...  All opinions, findings, conclusions and recommendations in this paper are those of the authors and do not necessarily reflect the views of the funding agencies.  ... 
doi:10.1145/1353343.1353423 dblp:conf/edbt/ZengNPWVC08 fatcat:zvn2svansbgipe25v256m3h5t4

SynFind: Compiling Syntenic Regions across Any Set of Genomes on Demand

Haibao Tang, Matthew D. Bomhoff, Evan Briones, Liangsheng Zhang, James C. Schnable, Eric Lyons
2015 Genome Biology and Evolution  
Deployed on the CoGe online platform, SynFind is connected to the genomic data from over 15,000 organisms from all domains of life as well as supporting multiple releases of the same organism.  ...  Given one query genome, SynFind is capable of identifying conserved syntenic regions in any set of target genomes.  ...  They also thank Zhenghui Zhong for providing help in benchmarking the performance of SynFind. They declare that they have no competing interests.  ... 
doi:10.1093/gbe/evv219 pmid:26560340 pmcid:PMC4700967 fatcat:bgq3ykdfdneftiyfnjnunhk3qe

MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity

Y. Wang, H. Tang, J. D. DeBarry, X. Tan, J. Li, X. Wang, T.-h. Lee, H. Jin, B. Marler, H. Guo, J. C. Kissinger, A. H. Paterson
2012 Nucleic Acids Research  
MCScan is an algorithm able to scan multiple genomes or subgenomes in order to identify putative homologous chromosomal regions, and align these regions using genes as anchors.  ...  The MCScanX toolkit implements an adjusted MCScan algorithm for detection of synteny and collinearity that extends the original software by incorporating 14 utility programs for visualization of results  ...  We summarized the functions of synteny and collinearity detection tools regarding five elements: graphic visualization, operation on multiple (>2) genomes, multialignments, evolutionary analyses of synteny  ... 
doi:10.1093/nar/gkr1293 pmid:22217600 pmcid:PMC3326336 fatcat:jcikkr34z5cgpias5rmew25zqq

An Overview of Duplicated Gene Detection Methods: Why the Duplication Mechanism Has to Be Accounted for in Their Choice

Tanguy Lallemand, Martin Leduc, Claudine Landès, Carène Rizzon, Emmanuelle Lerat
2020 Genes  
Various processes are known to allow a gene to be duplicated and different models explain how duplicated genes can be maintained in genomes.  ...  In this review, we first describe the evolutionary processes allowing the formation of duplicated genes but also describe the various bioinformatic approaches that can be used to identify them in genome  ...  Synteny portal [199] and Genomicus [200] provide also syntenic blocks generated by inferCars [201] for different species but also multiple visualizations.  ... 
doi:10.3390/genes11091046 pmid:32899740 pmcid:PMC7565063 fatcat:mdx7nygkibd2lfhvutcmd7bhz4

G-NEST: a gene neighborhood scoring tool to identify co-conserved, co-expressed genes

Danielle G Lemay, William F Martin, Angie S Hinrichs, Monique Rijnkels, J Bruce German, Ian Korf, Katherine S Pollard
2012 BMC Bioinformatics  
Given the genes within each potential neighborhood and syntenic blocks for organisms of interest, a Synteny Score (SS) is computed as the proportion of genomes in which the synteny of the neighborhood  ...  Given the petabytes of information now aligned with genome sequence, the scores produced by G-NEST can be uploaded to the Genome Browser and visualized in the context of this data.  ...  Authors' contributions DGL conceived of the study, participated in its design, implemented and executed all experiments, interpreted results, and drafted the manuscript.  ... 
doi:10.1186/1471-2105-13-253 pmid:23020263 pmcid:PMC3575404 fatcat:2pbe5dpez5espl6j7hnfy3cp3y

Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future

Georgios A. Pavlopoulos, Dimitris Malliarakis, Nikolas Papanikolaou, Theodosis Theodosiou, Anton J. Enright, Ioannis Iliopoulos
2015 GigaScience  
Here we discuss the past, present and future of genomic and systems biology visualization. We briefly comment on many visualization and analysis tools and the purposes that they serve.  ...  This widely used adage sums up in a few words the notion that a successful visual representation of a concept should enable easy and rapid absorption of large amounts of information.  ...  multidimensional cancer genomics datasets http://cbioportal.org Web-based Cinteny [256] Detection of syntenic regions across multiple genomes and measuring the extent of genome rearrangement using  ... 
doi:10.1186/s13742-015-0077-2 pmid:26309733 pmcid:PMC4548842 fatcat:w7hxgunagfcbxctnio7kwnucsy

Kerfuffle: a web tool for multi-species gene colocalization analysis

Robert Aboukhalil, Bernard Fendler, Gurinder S Atwal
2013 BMC Bioinformatics  
This software allows for flexibility and quick investigations of a user-defined set of genes, and the results may be saved online for further analysis.  ...  Results: Kerfuffle is a web tool designed to help discover, visualize, and quantify the physical organization of genomes by identifying significant gene colocalization and conservation across the assembled  ...  Acknowledgements We gratefully thank Peter Andrews for technical assistance with the web server and Ying Cai for useful comments on the web tool.  ... 
doi:10.1186/1471-2105-14-22 pmid:23327649 pmcid:PMC3598493 fatcat:ilgba5a3m5crxnqde6vzl54mee

BOV – a web-based BLAST output visualization tool

Rajesh Gollapudi, Kashi Revanna, Chris Hemmerich, Sarah Schaack, Qunfeng Dong
2008 BMC Genomics  
In order to manage and interpret the results of batch queries, a host of software packages have been developed to assist with data management and post-processing.  ...  Conclusion: BOV provides a user-friendly web interface to visualize the standard BLAST output for investigating wide-ranging genomic problems, including single query and batch query datasets.  ...  Acknowledgements This work was supported in part by the Indiana METACyt Initiative of Indiana University, funded in part through a major grant from the Lilly Endowment, Inc.  ... 
doi:10.1186/1471-2164-9-414 pmid:18793422 pmcid:PMC2566317 fatcat:ltmmctktwvachlkqga46bqsz2q

MicroSyn: A user friendly tool for detection of microsynteny in a gene family

Bin Cai, Xiaohan Yang, Gerald A Tuskan, Zong-Ming Cheng
2011 BMC Bioinformatics  
Results: We introduce MicroSyn software as a means of detecting microsynteny in adjacent genomic regions surrounding genes in gene families.  ...  Conclusions: Case studies of the microRNA167 genes in plants and Xyloglucan ndotransglycosylase/Hydrolase family in Populus trichocarpa were presented to show the utility of the software.  ...  Department of Energy Bioenergy Research Center supported by the Office of Biological and Environmental Research in the DOE Office of Science.  ... 
doi:10.1186/1471-2105-12-79 pmid:21418570 pmcid:PMC3072343 fatcat:sonmcx6yczfw3k2l4do4lcpoya

Unraveling genomic variation from next generation sequencing data

Georgios A Pavlopoulos, Anastasis Oulas, Ernesto Iacucci, Alejandro Sifrim, Yves Moreau, Reinhard Schneider, Jan Aerts, Ioannis Iliopoulos
2013 BioData Mining  
We conclude with a thorough review of tools developed to efficiently store, analyze and visualize such data with emphasis in structural variation analysis and comparative genomics.  ...  While NGS techniques stand as key players in modern biological research, the analysis and the interpretation of the vast amount of data that gets produced is a not an easy or a trivial task and still remains  ...  and allows path tracing between any two points. • Simultaneous visualization of multiple organisms related by a phylogeny. • 3D models of circular and linear chromosomes Sybil [122] Comparative genome  ... 
doi:10.1186/1756-0381-6-13 pmid:23885890 pmcid:PMC3726446 fatcat:l4ethjk2jjb5xlwpaw6vquwrqi

invis: Exploring high-dimensional RNA sequences from in vitro selection

Cagatay Demiralp, Eric Hayden, Jeff Hammerbacher, Jeffrey Heer
2013 2013 IEEE Symposium on Biological Data Visualization (BioVis)  
We present invis, the first visual analysis tool to facilitate exploration of in vitro selection sequence spaces. invis introduces a novel configuration of coordinated views that enables simultaneous inspection  ...  It allows scientists to isolate related sequences for further data analysis, compare sequence populations over varying conditions, filter sequences based on their similarities, and visualize likely pathways  ...  ACKNOWLEDGMENTS We thank Diana MacLean and Stuart K. Card for their feedback on earlier drafts of this paper.  ... 
doi:10.1109/biovis.2013.6664340 dblp:conf/biovis/DemiralpHHH13 fatcat:zncm32aeifamxg4seznqidv55e

Scalable Set Visualizations (Dagstuhl Seminar 17332)

Yifan Hu, Luana Micallef, Martin Nöllenburg, Peter Rodgers, Marc Herbstritt
2018 Dagstuhl Reports  
This report documents the program and outcomes of Dagstuhl Seminar 17332 "Scalable Set Visualizations", which took place August 14-18, 2017.  ...  The interdisciplinary seminar brought together 26 researchers from different areas in computer science and beyond such as information visualization, human-computer interaction, graph drawing, algorithms  ...  On behalf of all participants the organizers want to express their deep gratitude to the entire Dagstuhl staff for their outstanding support and service accompanying this seminar.  ... 
doi:10.4230/dagrep.7.8.1 dblp:journals/dagstuhl-reports/HuMNR17 fatcat:mqpltfdoqzaqfekr6yzxtprxsy