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MSAViewer: interactive JavaScript visualization of multiple sequence alignments

Guy Yachdav, Sebastian Wilzbach, Benedikt Rauscher, Robert Sheridan, Ian Sillitoe, James Procter, Suzanna E. Lewis, Burkhard Rost, Tatyana Goldberg
2016 Bioinformatics  
"MSAViewer: interactive JavaScript visualization of multiple sequence alignments." Bioinformatics 32 (22): 3501-3503.  ...  Abstract Summary: The MSAViewer is a quick and easy visualization and analysis JavaScript component for Multiple Sequence Alignment data of any size.  ...  Introduction Multiple Sequence Alignment (MSA) is a fundamental procedure to capture similarities between sequences of nucleotides (DNA/RNA) or of amino acids (protein).  ... 
doi:10.1093/bioinformatics/btw474 pmid:27412096 pmcid:PMC5181560 fatcat:cfhka6nwgvfqdkfq26y3jqk4n4

ProteoVision: web server for advanced visualization of ribosomal proteins

Petar I Penev, Holly M McCann, Caeden D Meade, Claudia Alvarez-Carreño, Aparna Maddala, Chad R Bernier, Vasanta L Chivukula, Maria Ahmad, Burak Gulen, Aakash Sharma, Loren Dean Williams, Anton S Petrov
2021 Nucleic Acids Research  
Starting with a multiple sequence alignment, ProteoVision computes conservation scores and a variety of physicochemical properties and simultaneously maps and visualizes alignments and other data on multiple  ...  ProteoVision is a web server designed to explore protein structure and evolution through simultaneous visualization of multiple sequence alignments, topology diagrams and 3D structures.  ...  Rohan Gupta, Joshua Lin, the group of Prof. George E. Fox, and Yulia Dumov, whose input has been invaluable to our work.  ... 
doi:10.1093/nar/gkab351 pmid:33999189 fatcat:ih4x3uftpvhaxmvw55cnysjcwy

AlignmentViewer: Sequence Analysis of Large Protein Families [article]

Roc Reguant, Yevgeniy Antipin, Rob Sheridan, Augustin Luna, Chris Sander
2018 bioRxiv   pre-print
AlignmentViewer is multiple sequence alignment viewer for protein families with flexible visualization, analysis tools and links to protein family databases.  ...  of functionally constrained interactions.  ...  The project was supported by the Human Frontier Science Program (HFSP), the National Resource for Network Biology (NRNB), the Department of Cell Biology at HMS and the NIGMS.  ... 
doi:10.1101/269720 fatcat:a5ncpgp4ynbwrlyfdf7klb7psi

MSABrowser: dynamic and fast visualization of sequence alignments, variations, and annotations [article]

Furkan M. Torun, Halil I. Bilgin, Oktay I. Kaplan
2021 bioRxiv   pre-print
Sequence alignment is an excellent way to visualize the similarities and differences between DNA, RNA, or protein sequences, yet it is currently difficult to jointly view sequence alignment data with genetic  ...  sequence alignments.  ...  Yachdav,G. et al. (2016) MSAViewer: interactive JavaScript visualization of multiple sequence alignments. Bioinformatics, btw474.  ... 
doi:10.1101/2021.04.05.426321 fatcat:gai3yxp5vzfcfdh65gwvzregki

AlignmentViewer: Sequence Analysis of Large Protein Families

Roc Reguant, Yevgeniy Antipin, Rob Sheridan, Christian Dallago, Drew Diamantoukos, Augustin Luna, Chris Sander, Nicholas Paul Gauthier
2020 F1000Research  
AlignmentViewer is a web-based tool to view and analyze multiple sequence alignments of protein families.  ...  The particular strengths of AlignmentViewer include flexible visualization at different scales as well as analysis of conservation patterns and of the distribution of proteins in sequence space.  ...  MSAViewer is an interactive MSA visualizer in JavaScript that implements basic features of viewing, scrolling and motif selection.  ... 
doi:10.12688/f1000research.22242.1 pmid:33123346 pmcid:PMC7570326 fatcat:25afyx6nfjds7pqc5qjv2gvpby

Web Apps Come of Age for Molecular Sciences

Luciano Abriata
2017 Informatics  
out numerical calculations, text processing and mining, retrieval and analysis of data through queries to online databases and web services, effective visualization of data including 3D visualization  ...  and analyze the content delivered to their devices on-the-fly and interactively.  ...  Conflicts of Interest: The author declares no conflict of interest.  ... 
doi:10.3390/informatics4030028 fatcat:xrz2ijpkdzfjfna43x6nexocam

PanACEA: a bioinformatics tool for the exploration and visualization of bacterial pan-chromosomes

Thomas H. Clarke, Lauren M. Brinkac, Jason M. Inman, Granger Sutton, Derrick E. Fouts
2018 BMC Bioinformatics  
Bacterial pan-genomes, comprised of conserved and variable genes across multiple sequenced bacterial genomes, allow for identification of genomic regions that are phylogenetically discriminating or functionally  ...  Conclusions: PanACEA can rapidly translate the results of pan-chromosome programs into an intuitive and interactive visual representation.  ...  Funding This project has been funded in whole or part with federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services  ... 
doi:10.1186/s12859-018-2250-y pmid:29945570 pmcid:PMC6020400 fatcat:qbm5m6vmvrempcfcsyfaaqpu34

MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization

Kazutaka Katoh, John Rozewicki, Kazunori D. Yamada
2017 Briefings in Bioinformatics  
This article describes several features in the MAFFT online service for multiple sequence alignment (MSA).  ...  Multiple sequence alignment (MSA) is an important step in comparative analyses of biological sequences. We provide an online service for computing MSAs on the Web using MAFFT [1, 2] .  ...  To visualize MSAs, two tools, Jalview [38] (as Java plugin) and MSAViewer [39] (written in JavaScript; Figure 3C ), are available on our service.  ... 
doi:10.1093/bib/bbx108 pmid:28968734 fatcat:hkwh5tskjbc2hith2rhnmuyrci

Alignment of Biological Sequences with Jalview [chapter]

James B. Procter, G. Mungo Carstairs, Ben Soares, Kira Mourão, T. Charles Ofoegbu, Daniel Barton, Lauren Lui, Anne Menard, Natasha Sherstnev, David Roldan-Martinez, Suzanne Duce, David M. A. Martin (+1 others)
2020 Msphere  
In this chapter, we introduce core functionality of the Jalview interactive platform for the creation, analysis, and publication of multiple sequence alignments.  ...  The accompanying notes provide background information on the underlying methods and discuss additional options for working with Jalview to perform multiple sequence alignment, functional site analysis,  ...  Development of the Jalview sequence analysis platform is coordinated at the University of Dundee with support from the UK's Biotechnology and Biological Sciences Research Council (BB/L010742/1), the Scottish  ... 
doi:10.1007/978-1-0716-1036-7_13 pmid:33289895 pmcid:PMC7116599 fatcat:skgegj4e2rdmhb2nm5gfcurew4

REDIdb 3.0: A Comprehensive Collection of RNA Editing Events in Plant Organellar Genomes

Claudio Lo Giudice, Graziano Pesole, Ernesto Picardi
2018 Frontiers in Plant Science  
sequence alignments.  ...  It was first discovered in kinetoplastid protozoa followed by its reporting in a wide range of organisms.  ...  Multiple sequence alignments of edited cDNAs and proteins have been generated by ClustalOmega (Sievers et al., 2011) and displayed in html pages through the MSAViewer (Yachdav et al., 2016) , a JavaScript  ... 
doi:10.3389/fpls.2018.00482 pmid:29696033 pmcid:PMC5904370 fatcat:qyabjm7ngneyje4w7dntfbpska

ChlamBase: a curated model organism database for the Chlamydia research community

2019 Database: The Journal of Biological Databases and Curation  
The accelerating growth of genomic and proteomic information for Chlamydia species, coupled with unique biological aspects of these pathogens, necessitates bioinformatic tools and features that are not  ...  In addition, a key feature of ChlamBase is that it empowers users in the field to contribute new annotations and data as the field advances with continued discoveries.  ...  This module delegates multiple alignments to the external web service MUSCLE (18) and subsequently displays the results in the JavaScript widget MSAViewer for interactive navigation of aligned sequences  ... 
doi:10.1093/database/baz041 pmid:30985891 pmcid:PMC6463448 fatcat:qtflnse2zreyfpqmwp6ibm6o5m

CottonFGD: an integrated functional genomics database for cotton

Tao Zhu, Chengzhen Liang, Zhigang Meng, Guoqing Sun, Zhaoghong Meng, Sandui Guo, Rui Zhang
2017 BMC Plant Biology  
Conclusion: Equipped with specialized functional modules and modernized visualization tools, and populated with multiple kinds of -omics data, CottonFGD provides a quick and easy-to-use data analysis platform  ...  marker data, transcriptome data, and population genome resequencing data for all four of the sequenced Gossypium species.  ...  Yin (Institute of Crop Sciences, Chinese Academy of Agricultural Sciences) for his help on network construction, and the anonymous reviewers for their useful suggestions to improve the manuscript.  ... 
doi:10.1186/s12870-017-1039-x pmid:28595571 pmcid:PMC5465443 fatcat:zej3pp4kbzh45gcxksgkqx7tr4

Swiss-PO: a new tool to analyze the impact of mutations on protein three-dimensional structures for precision oncology

Fanny S. Krebs, Vincent Zoete, Maxence Trottet, Timothée Pouchon, Christophe Bovigny, Olivier Michielin
2021 npj Precision Oncology  
Swiss-PO is constructed around a manually curated database of 3D structures, variant annotations, and sequence alignments, for a list of 50 genes taken from the Ion AmpliSeq TM Custom Cancer Hotspot Panel  ...  The importance of the mutated residue for the structure and activity of the protein can be assessed based on the molecular interactions exchanged with neighbor residues in 3D within the same protein or  ...  The authors would like to thank the Swiss-Prot group of the SIB Swiss Institute of Bioinformatics for mutations data.  ... 
doi:10.1038/s41698-021-00156-5 pmid:33737716 fatcat:kqfctcyb25bwpk34sekbpqtcei

T1TAdb: the database of Type I Toxin-Antitoxin systems

Nicolas J Tourasse, Fabien Darfeuille
2021 RNA: A publication of the RNA Society  
It also includes tools for comparative analysis, such as sequence similarity search and computation of structural multiple alignments, which are annotated with covariation information.  ...  To our knowledge, T1TAdb represents the largest collection of features, sequences, and structural annotations on this class of genetic modules.  ...  The web server hosting T1TAdb is provided by the ODS Web Hosting service of CNRS. We thank Dr. Stéphane Thore and Dr. Sébastien Fribourg for providing additional computing power.  ... 
doi:10.1261/rna.078802.121 pmid:34531327 pmcid:PMC8594479 fatcat:6rwknj5mpjer7f7dh533sfcaou

RampDB: a web application and database for the exploration and prediction of receptor activity modifying protein interactions

Nadav Topaz, Nazia Mojib, Aroon T. Chande, Julia Kubanek, I. King Jordan
2017 Database: The Journal of Biological Databases and Curation  
The RampDB search utility allows users to explore known RAMP interactions, or to predict novel interactions, via either protein sequence (bioinformatic) or ligand (chemoinformatic) queries.  ...  RAMPs function by interacting with the N-termini and transmembrane domains of GPCRs, and the receptor phenotypes of the resulting complexes are determined by the specific isoform of the interacting RAMPs  ...  Acknowledgements We would like to thank members of the Julia Kubanek (Georgia Institute of Technology) and Nael McCarty (Emory University) laboratories for discussions and guidance related to receptor  ... 
doi:10.1093/database/bax067 pmid:29220456 pmcid:PMC5737055 fatcat:d5ap36mzz5hgfkgdfounwpghhq
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