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Viewing and annotating sequence data with Artemis

M. Berriman
2003 Briefings in Bioinformatics  
Artemis is a widely used software tool for annotating and viewing sequence data. No database is required to use Artemis.  ...  Artemis allows annotated genomes to be easily browsed and makes it simple to add useful biological information to raw sequence data.  ...  Acknowledgments The development of Artemis is funded by the Wellcome Trust.  ... 
doi:10.1093/bib/4.2.124 pmid:12846394 fatcat:udylulbgzfbjraek265kck75ke

Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database

Tim Carver, Matthew Berriman, Adrian Tivey, Chinmay Patel, Ulrike Böhme, Barclay G. Barrell, Julian Parkhill, Marie-Adèle Rajandream
2008 Computer applications in the biosciences : CABIOS  
Motivation: Artemis and Artemis Comparison Tool (ACT) have become mainstream tools for viewing and annotating sequence data, particularly for microbial genomes.  ...  Since its first release, Artemis has been continuously developed and supported with additional functionality for editing and analysing sequences based on feedback from an active user community of laboratory  ...  We would like to thank Professor Christopher Newbold (University of Oxford Institute of Molecular Medicine) for his suggestions on improving the design of the Artemis Gene Builder.  ... 
doi:10.1093/bioinformatics/btn529 pmid:18845581 pmcid:PMC2606163 fatcat:mwl6kuzlcfeunlju73cov3rsm4

Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data

T. Carver, S. R. Harris, M. Berriman, J. Parkhill, J. A. McQuillan
2011 Bioinformatics  
Results: We present Artemis as a tool for integrated visualization and computational analysis of different types of HTS datasets in the context of a reference genome and its corresponding annotation.  ...  Availability: Artemis is freely available (under a GPL licence) for download (for MacOSX, UNIX and Windows) at the Wellcome Trust Sanger Institute websites:  ...  The original Artemis used a memory-based approach, where all the sequence and annotation data was loaded into memory.  ... 
doi:10.1093/bioinformatics/btr703 pmid:22199388 pmcid:PMC3278759 fatcat:57t7vj3jn5c2rcb3uliyxjxnxy

BamView: viewing mapped read alignment data in the context of the reference sequence

T. Carver, U. Bohme, T. D. Otto, J. Parkhill, M. Berriman
2010 Bioinformatics  
BamView has also been integrated into Artemis so that the reads can be viewed in the context of the nucleotide sequence and genomic features.  ...  It can be used in a number of contexts including SNP calling and structural annotation.  ...  Artemis is a freely available genome browser and annotation tool. BamView in Artemis provides the annotator with an extra level of information that can inform them about structural annotation.  ... 
doi:10.1093/bioinformatics/btq010 pmid:20071372 pmcid:PMC2828118 fatcat:ewjujt5lsbdcfpdhyaeb7mav4i

BamView: visualizing and interpretation of next-generation sequencing read alignments

T. Carver, S. R. Harris, T. D. Otto, M. Berriman, J. Parkhill, J. A. McQuillan
2012 Briefings in Bioinformatics  
As well as being a standalone application it can be used as an integrated part of the Artemis genome browser, BamView allows the user to study NGS data in the context of the sequence and annotation of  ...  To enable in-depth investigation of NGS data, various views are provided that can be configured to highlight interesting aspects of the data.  ...  Another application for Artemis BamView is to correct reference sequence annotation using RNA-Seq data.  ... 
doi:10.1093/bib/bbr073 pmid:22253280 pmcid:PMC3603209 fatcat:kro24phha5hthoyopfyddnpd6i

Chado Controller: advanced annotation management with a community annotation system

Valentin Guignon, Gaëtan Droc, Michael Alaux, Franc-Christophe Baurens, Olivier Garsmeur, Claire Poiron, Tim Carver, Mathieu Rouard, Stéphanie Bocs
2012 Computer applications in the biosciences : CABIOS  
We developed a controller that is compliant with the Chado database schema, GBrowse and genome annotation-editing tools such as Artemis and Apollo.  ...  It enables the management of public and private data, monitors manual annotation (with controlled vocabularies, structural and functional annotation controls) and stores versions of annotation for all  ...  ACKNOWLEDGEMENTS We would like to acknowledge and thank the GMOD and GNPAnnot communities in particular to Fabrice Legeai, Joelle Amselem and Baptiste Brault.  ... 
doi:10.1093/bioinformatics/bts046 pmid:22285827 pmcid:PMC3315714 fatcat:xd755nerbnbmtpymvereiobw2a

GeneDB--an annotation database for pathogens

F. J. Logan-Klumpler, N. De Silva, U. Boehme, M. B. Rogers, G. Velarde, J. A. McQuillan, T. Carver, M. Aslett, C. Olsen, S. Subramanian, I. Phan, C. Farris (+16 others)
2011 Nucleic Acids Research  
ACKNOWLEDGEMENTS The authors wish to acknowledge the contribution of numerous members of the parasitology research community, in the form of advice, suggestions and/or data.  ...  More detailed views of the structure and annotation are available through Artemis and Web-Artemis buttons.  ...  Currently short-read alignments can be viewed using Artemis BAMview (5), and more recently pileup format files, converted to VCF, can now be viewed with Artemis VCFview.  ... 
doi:10.1093/nar/gkr1032 pmid:22116062 pmcid:PMC3245030 fatcat:4znikrcq3zbxjizxzokpcjullm

Meeting report: a workshop on Best Practices in Genome Annotation

R. Madupu, L. M. Brinkac, J. Harrow, L. G. Wilming, U. Bohme, P. Lamesch, L. I. Hannick
2010 Database: The Journal of Biological Databases and Curation  
(A) Artemis main view sequence panel. (B) The Comparison view. This panel displays the regions of similarity (TBLASTX comparison) between two sequences.  ...  Artemis can be used to simultaneously view the results of multiple sequence analysis in the context of a genome sequence.  ... 
doi:10.1093/database/baq001 pmid:20428316 pmcid:PMC2860899 fatcat:ibdlwzv74veqrb6mzl7nkyr3km

TparvaDB: a database to support Theileria parva vaccine development

P. Visendi, W. Ng'ang'a, W. Bulimo, R. Bishop, J. Ochanda, E. P. de Villiers
2011 Database: The Journal of Biological Databases and Curation  
We implemented an online annotation functionality using Artemis, a DNA sequence viewer and annotation tool (13) .  ...  The original T. parva genome data and the mapped EST data were visualized and gene models manually annotated using Artemis.  ... 
doi:10.1093/database/bar015 pmid:21546359 pmcid:PMC3092609 fatcat:6apwkmtf5ba75k6y7skqsf6jm4

ASAP: a resource for annotating, curating, comparing, and disseminating genomic data

J. D. Glasner
2006 Nucleic Acids Research  
ASAP is being used for a large-scale effort to augment and curate annotations for genomes of enterobacterial pathogens and for additional genome sequences.  ...  ASAP is a comprehensive web-based system for community genome annotation and analysis.  ...  ACKNOWLEDGEMENTS We would like to thank the Handelsman lab for using ASAP to test annotation of their metagenomics BAC sequences and the Talaat lab for using the system in their research.  ... 
doi:10.1093/nar/gkj164 pmid:16381899 pmcid:PMC1347526 fatcat:tajtxoef25chrcnupbixowykae

Importing statistical measures into Artemis enhances gene identification in the Leishmania genome project

Gautam Aggarwal, E A Worthey, Paul D McDonagh, Peter J Myler
2003 BMC Bioinformatics  
At SBRI, chromosomal sequence is annotated using a combination of trained and untrained non-consensus gene-prediction algorithms with ARTEMIS, an annotation platform with rich and user-friendly interfaces  ...  Here we describe a methodology used to import results from three different protein-coding gene-prediction algorithms (GLIMMER, TESTCODE and GENESCAN) into the ARTEMIS sequence viewer and annotation tool  ...  Acknowledgements The authors thank Kim Rutherford (Wellcome Trust Sanger Institute) for the help and useful discussion. This work was supported by NIH grant AI40599.  ... 
doi:10.1186/1471-2105-4-23 pmid:12793912 pmcid:PMC165441 fatcat:torx4lbvmvaz3h4vylf6kxuu6q

ACT: the Artemis comparison tool

T. J. Carver, K. M. Rutherford, M. Berriman, M.-A. Rajandream, B. G. Barrell, J. Parkhill
2005 Bioinformatics  
The Artemis Comparison Tool (ACT) allows an interactive visualisation of comparisons between complete genome sequences and associated annotations.  ...  The comparison data can be generated with several different programs; BLASTN, TBLASTX or Mummer comparisons between genomic DNA sequences, or orthologue tables generated by reciprocal FASTA comparison  ...  Comparative genomics is an increasingly important step in the annotation and analysis process, allowing phenotypic differences between strains and species to be correlated with changes in the chromosomes  ... 
doi:10.1093/bioinformatics/bti553 pmid:15976072 fatcat:vlsgzvcnibfcpbe5zgwpsswho4

NOVEL GENE IDENTIFICATION USING THE TRANSPOSE ELEMENTS IN RHODOCOCCUS AETHERIVORANS PLASMID PRA3 FOR FUTURE NOVEL DRUG GENE TESTING

Mishal Al Ammar Anas Alfadda
2020 Zenodo  
Genome annotation has a huge impact in molecular biology, therefore making an annotated data base using Artemis the genome browser program will allow certain researchers to have a database that they can  ...  Using a program called Artemis, we created a database from a plasmid in bacteria called Rhodococcus aetherivorans which contains 350,000 base pairs and contains 207 genes.  ...  It is the main tool in annotating and viewing sequenced data in microbial genomes. It became famous in 2002. It has become the main tool in annotating pathogenic microbial genomes.  ... 
doi:10.5281/zenodo.3600269 fatcat:v2mlweaqlnearino3vmntofmma

WebACT--an online companion for the Artemis Comparison Tool

J. C. Abbott, D. M. Aanensen, K. Rutherford, S. Butcher, B. G. Spratt
2005 Bioinformatics  
WebACT is an online resource which enables the rapid provision of simultaneous BLAST comparisons between up to five genomic sequences in a format amenable for visualization with the well-known Artemis  ...  Comparison and sequence files, whether computed online or retrieved from the database of pre-computed genome comparisons, can be viewed online using ACT and are available for download.  ...  This work was supported by the Faculties of Life Sciences and Medicine, Imperial College London and the Wellcome Trust. Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/bti601 pmid:16076890 fatcat:6y4khffbdrajjkbh6uunxvosua

Curation of the Plasmodium falciparum genome

Andrew E. Berry, Malcolm J. Gardner, Gert-Jan Caspers, David S. Roos, Matthew Berriman
2004 Trends in Parasitology  
We offer the widest and deepest coverage in a range of media types to enhance cross-pollination of information, breakthroughs in research and discovery, and the sharing and preservation of knowledge.  ...  has had a makeover, inside and out.  ...  PlasmoDB was established with support from the Burroughs Wellcome Fund, and is now supported by the NIH. GeneDB is funded by the Wellcome Trust Sanger Institute.  ... 
doi:10.1016/j.pt.2004.09.003 pmid:15522662 fatcat:xdwq5sjro5a7pfv4sytnuiqxwy
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