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CGAT: a comparative genome analysis tool for visualizing alignments in the analysis of complex evolutionary changes between closely related genomes

Ikuo Uchiyama, Toshio Higuchi, Ichizo Kobayashi
2006 BMC Bioinformatics  
We have developed a comparative genome analysis tool, named CGAT, which allows detailed comparisons of closely related bacteria-sized genomes mainly through visualizing middle-to-large-scale changes to  ...  However, although numerous alignment calculation and visualization tools have been developed to date, the analysis of complex genomic changes, such as large insertions, deletions, inversions, translocations  ...  The work in the laboratory of IK was supported by the 21 st century COE project of "Elucidation of Language Structure and Semantic behind Genome and Life System" and by Grants-in-Aid for Scientific Research  ... 
doi:10.1186/1471-2105-7-472 pmid:17062155 pmcid:PMC1643837 fatcat:x7atbod4dvagth62h3myl52yfu

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.  ...  in comparative genomics data.  ... 
doi:10.1186/s13742-015-0077-2 pmid:26309733 pmcid:PMC4548842 fatcat:w7hxgunagfcbxctnio7kwnucsy

PLATCOM: Current Status and Plan for the Next Stages [chapter]

Kwangmin Choi, Jeong-Hyeon Choi, Amit Saple, Zhiping Wang, Jason Lee, Sun Kim
2005 Lecture Notes in Computer Science  
We have been developing a system for comparing multiple genomes, PLATCOM, where users can choose genomes of their choice freely and perform analysis of the selected genomes with a suite of computational  ...  Comparison of multiple genomes is a challenging task since combining multiple tools for sequence analysis requires a significant amount of programming work and knowledge on each tool.  ...  We plan to include more tools. With the databases and sequence analysis tools, genome can be compared.  ... 
doi:10.1007/11530084_27 fatcat:erlumy5g6vfltp73qn6ojzagnu

RepViz: a replicate-driven R tool for visualizing genomic regions

Thomas Faux, Kalle T. Rytkönen, Asta Laiho, Laura L. Elo
2019 BMC Research Notes  
Visualization of sequencing data is an integral part of genomic data analysis.  ...  Although there are several tools to visualize sequencing data on genomic regions, they do not offer user-friendly ways to view simultaneously different groups of replicates.  ...  In an effort to provide a user-friendly tool to visualize groups of replicates on genomic regions, we propose a replicate-driven R tool, RepViz.  ... 
doi:10.1186/s13104-019-4473-z pmid:31324268 pmcid:PMC6642542 fatcat:snwla72ahzdyven3kpxln3uuie

Dynamic visualization and comparative analysis of multiple collinear genomic data

Jeremy Wang, Fernando Pardo-Manuel de Villena, Leonard McMillan
2011 Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine - BCB '11  
We have developed a novel tool for visualizing and analyzing multiple collinear genomes. Unlike previous genome browsers and viewers, ours allows for simultaneous and comparative analysis.  ...  Comparative analysis is facilitated through reordering and clustering of tracks, which can vary throughout the genome.  ...  We use our tool to visualize eight different data types to aid in comparative analysis of these 198 mouse samples.  ... 
doi:10.1145/2147805.2147846 pmid:29119144 pmcid:PMC5672797 dblp:conf/bcb/WangVM11 fatcat:gzuu642xgjdodokhghbnnhvxsy

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  ...  visualization tools are carefully tailored to the specialized analysis demands of their users, and it is unlikely that a universal tool for genomics analysis is feasible or desirable.  ... 
doi:10.1038/nmeth.1422 pmid:20195257 fatcat:3gxjhrkvxzfzllbxk4jt4vll2m

GenomeGems: evaluation of genetic variability from deep sequencing data

Sharon Ben-Zvi, Adi Givati, Noam Shomron
2012 BMC Research Notes  
The tool allows the user to compare and visualize SNPs from multiple experiments and to easily load SNP data onto the UCSC Genome browser for further detailed information.  ...  As such, via automatic, clear and accessible presentation of processed Deep Sequencing data, our tool aims to facilitate ranking of genomic SNP calling.  ...  The tool allows the user to compare and visualize SNPs from multiple experiments and to easily load SNP data onto the UCSC Genome browser for further detailed information.  ... 
doi:10.1186/1756-0500-5-338 pmid:22748151 pmcid:PMC3499170 fatcat:bedz7il7krg6ffsufgtzlwytfe

Comparative analysis and visualization of multiple collinear genomes

Jeremy R Wang, Fernando Pardo-Manuel de Villena, Leonard McMillan
2012 BMC Bioinformatics  
However, existing genome browsers and visualization tools are not wellsuited to perform meaningful comparative analysis among a large number of genomes.  ...  Conclusions: Unlike previous genome browsers and viewers, ours allows for simultaneous and comparative analysis.  ...  Acknowledgements Funding provided in part by grants from the National Institutes of Health (NIH P50 GM 076468, P50 HG 006582, U54 AI 081680) and NSF project grant "Visualizing and Exploring High-dimensional  ... 
doi:10.1186/1471-2105-13-s3-s13 pmid:22536897 pmcid:PMC3311102 fatcat:pjz7im3bufgdpg4sdy7mkyzjbu

VISTA: computational tools for comparative genomics

K. A. Frazer, L. Pachter, A. Poliakov, E. M. Rubin, I. Dubchak
2004 Nucleic Acids Research  
Currently the VISTA site includes multiple comparative genomics tools and provides users with rich capabilities to browse pre-computed wholegenome alignments of large vertebrate genomes and other groups  ...  of organisms with VISTA Browser, to submit their own sequences of interest to several VISTA servers for various types of comparative analysis and to obtain detailed comparative analysis results for a  ...  ACKNOWLEDGEMENTS We are grateful to Simon Minovitsky, Shyam Prabhakar, Michael Teplitsky and Dmitriy Ryaboy for ongoing development, maintenance and support of all our tools.  ... 
doi:10.1093/nar/gkh458 pmid:15215394 pmcid:PMC441596 fatcat:p2s6nshky5alrhnrlvxo5ii4va

GenomeVISTA—an integrated software package for whole-genome alignment and visualization

Alexandre Poliakov, Justin Foong, Michael Brudno, Inna Dubchak
2014 Computer applications in the biosciences : CABIOS  
for comparative analysis.  ...  Our VISTA family of tools for comparative genomics, based on algorithms for pairwise and multiple alignments of genomic sequences and whole-genome assemblies, has become one of the standard techniques  ...  DISCUSSION GenomeVISTA unifies in one package multiple capabilities necessary to carry out various types of comparative analysis of genomic sequences and whole-genome assemblies.  ... 
doi:10.1093/bioinformatics/btu355 pmid:24860159 pmcid:PMC4155257 fatcat:yhc4w7oh5vacvjglhnyt5aivye

NGS analyses by visualization with Trackster

Jeremy Goecks, Nate Coraor, The Galaxy Team, Anton Nekrutenko, James Taylor
2012 Nature Biotechnology  
Visualization, then, cannot remain an endpoint for genomic analyses, but instead must be integrated with analysis tools so that visualization can be used to evaluate intermediate results and incrementally  ...  This approach breaks down for large genomic datasets where visualizing the results of timeconsuming, computationally intensive analyses often shows that different analysis settings need to be used.  ...  Additional funding is provided, in part, under a grant with the Pennsylvania Department of Health using Tobacco Settlement Funds.  ... 
doi:10.1038/nbt.2404 pmid:23138293 pmcid:PMC3889118 fatcat:ebuqqo6b6rbw3dks2eho37ugcu

Visualization tools for human structural variations identified by whole-genome sequencing

Toshiyuki T. Yokoyama, Masahiro Kasahara
2019 Journal of Human Genetics  
We hope that this review will serve as a guide for readers on the currently available SV visualization tools and lead to the development of new SV visualization tools in the near future.  ...  We first categorize the ways in which SV visualization tools display SVs into ten major categories, which we denote as view modules.  ...  Visualization tools in a large analysis pipeline There is an another class of visualization tools, shipped with large genome analysis pipelines.  ... 
doi:10.1038/s10038-019-0687-0 pmid:31666648 fatcat:7ctffnpxvne5ze56lgrcypjuca

zPicture: Dynamic Alignment and Visualization Tool for Analyzing Conservation Profiles

I. Ovcharenko
2004 Genome Research  
Finally, we describe how this tool can be efficiently applied to the analysis of nonvertebrate genomes, including those of microbial organisms. 6 Corresponding author.  ...  Comparative sequence analysis has evolved as an essential technique for identifying functional coding and noncoding elements conserved throughout evolution.  ...  Pip-Maker ; http://bio.cse.psu.edu/pipmaker/) and VISTA ; http://www-gsd.lbl.gov/VISTA/ VistaInput.html) are two alignment and visualization tools used extensively to perform comparative genomic analysis  ... 
doi:10.1101/gr.2129504 pmid:14993211 pmcid:PMC353235 fatcat:uky7p7jeergwdkhdon2naigm3y

CGAP: a new comprehensive platform for the comparative analysis of chloroplast genomes

Jinkui Cheng, Xu Zeng, Guomin Ren, Zhihua Liu
2013 BMC Bioinformatics  
However, no comprehensive platform or tool has been developed for the comparative and phylogenetic analysis of chloroplast genomes.  ...  CGAP integrated genome collection, visualization, content comparison, phylogeny analysis and annotation functions together.  ...  However, there is no comprehensive platform or tool which can be used for the comparative and phylogenetic analysis of chloroplast genomes.  ... 
doi:10.1186/1471-2105-14-95 pmid:23496817 pmcid:PMC3636126 fatcat:jjjnpq4h35dnlirczdh4qc25oi

Visualization of comparative genomic analyses by BLAST score ratio

David A Rasko, Garry S A Myers, Jacques Ravel
2005 BMC Bioinformatics  
This massive influx of data provides the opportunity to obtain biological insights through comparative genomics. However few tools are available for this scale of comparative analysis.  ...  The output of the BSR analysis enables global visualization of the degree of proteome similarity between all three genomes.  ...  The GenomeComp tool [6] displays a similar analysis also based on BLASTN E-values to compare genome sequences.  ... 
doi:10.1186/1471-2105-6-2 pmid:15634352 pmcid:PMC545078 fatcat:kz6u4oepejhyphwjnmumsgdtgu
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