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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.  ...  ACT uses Artemis components to display the sequences and so inherits powerful searching and analysis tools.  ...  ACT re-uses the Artemis (Rutherford et al., 2000 and Berriman et al., 2003) code to display the sequence and features. As a result it inherits a number of the tools and features of Artemis.  ... 
doi:10.1093/bioinformatics/bti553 pmid:15976072 fatcat:vlsgzvcnibfcpbe5zgwpsswho4

WebACT--an online companion for the Artemis Comparison Tool

J. C. Abbott, D. M. Aanensen, K. Rutherford, S. Butcher, B. G. Spratt
2005 Bioinformatics  
Comparison Tool (ACT).  ...  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  ...  ACKNOWLEDGEMENTS The authors are grateful to the London E-Science Centre (http://www. lesc.imperial.ac.uk) for access to high performance computing resources.  ... 
doi:10.1093/bioinformatics/bti601 pmid:16076890 fatcat:6y4khffbdrajjkbh6uunxvosua

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.  ...  Availability: Artemis and ACT are freely available (under a GPL licence) for download (for MacOSX, UNIX and Windows) at the Wellcome Trust Sanger Institute web sites:  ...  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

The Acts of the Apostles

J. M. H., William Mordaunt Furneaux
1912 The Irish Church Quarterly  
We use information technology and tools to increase productivity and facilitate new forms of scholarship. For more information about JSTOR, please contact support@jstor.org.  ...  Might not the list be extended, considering the class of reader aimed at, so as to include such names as Damaris, Patara, Aquila, Artemis, Melita.  ...  Hence the Acts cannot have been written much before A.D. 75."  ... 
doi:10.2307/30067737 fatcat:me5nqgfjcff75eapteuxkszp3i

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:  ...  ACKNOWLEDGEMENTS We thank Kim Wong at the WTSI for providing feedback on the Mouse Genomes dataset.  ... 
doi:10.1093/bioinformatics/btr703 pmid:22199388 pmcid:PMC3278759 fatcat:57t7vj3jn5c2rcb3uliyxjxnxy

ABACAS: algorithm-based automatic contiguation of assembled sequences

S. Assefa, T. M. Keane, T. D. Otto, C. Newbold, M. Berriman
2009 Bioinformatics  
. • Comparison file can be used to visualize ordered and oriented contigs in ACT, the Artemis Comparison Tool [3]. • Contigs that were not mapped can be included to the pseudomolecule. • Repetitive regions  ...  Et al. (1990) Basic local alignment search tool. J. Molecular Biology, 215:403-410.  ... 
doi:10.1093/bioinformatics/btp347 pmid:19497936 pmcid:PMC2712343 fatcat:q3bqwp77zfburlp6sxed32uap4

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  
See Table 2 for the comparison of the Zmap/Otterlace tool with Apollo and Artemis/ACT. Features.  ...  See Table 2 for the comparison of Artemis/ACT with Zmap/Otterlace and Apollo. Features.  ... 
doi:10.1093/database/baq001 pmid:20428316 pmcid:PMC2860899 fatcat:ibdlwzv74veqrb6mzl7nkyr3km

Beginner's guide to comparative bacterial genome analysis using next-generation sequence data

David J Edwards, Kathryn E Holt
2013 Microbial Informatics and Experimentation  
The main topics covered are assembly, ordering of contigs, annotation, genome comparison and extracting common typing information.  ...  High throughput sequencing is now fast and cheap enough to be considered part of the toolbox for investigating bacteria, and there are thousands of bacterial genome sequences available for comparison in  ...  Acknowledgements KEH is supported by Fellowship #628930 from the NHMRC of Australia.  ... 
doi:10.1186/2042-5783-3-2 pmid:23575213 pmcid:PMC3630013 fatcat:ddo7stt2cjabbphspbfyjecmci

Genome Annotation and Comparative Genomics of ORF Virus

A. K. M. Firoj Mahmud, K. M. Zillur Rahman, Shuvra Kanti Dey, Tahsina Islam, Ali Azam Talukder
2014 Advances in microbiology  
ORF virus (ORFV), the etiological agent of contagious pustular dermatitis in small ruminants, belongs to members of the genus Parapoxvirus of the Poxviridae.  ...  One of the ORF-039 contains signal peptide indicating the possibilities to be secretory protein coding gene.  ...  Acknowledgements The authors wish to thank Ministry of Education (17/10, M-15/2007/226 and HEQEP, CP-W1-3413), Bangladesh for partially funding this research work.  ... 
doi:10.4236/aim.2014.415122 fatcat:ctltxlikgvhk5g4nro7macpaoy

CompaGB: An open framework for genome browsers comparison

Thomas Lacroix, Valentin Loux, Annie Gendrault, Jean-François Gibrat, Hélène Chiapello
2011 BMC Research Notes  
Tools to visualize and explore genomes hold a central place in genomics and the diversity of genome browsers has increased dramatically over the last few years.  ...  evaluations, and (ii) a web resource providing numerous facilities either for visualizing comparisons or performing new evaluations.  ...  Acknowledgements We are grateful to the INRA MIGALE bioinformatics platform http://migale. jouy.inra.fr for providing us with help and support. We thank P. Bessières, C. Caron, M. Hoebeke, C.  ... 
doi:10.1186/1756-0500-4-133 pmid:21542900 pmcid:PMC3096945 fatcat:nuvzllunibcphph5c6fauebsvq

CONTIGuator: a bacterial genomes finishing tool for structural insights on draft genomes

Marco Galardini, Emanuele G Biondi, Marco Bazzicalupo, Alessio Mengoni
2011 Source Code for Biology and Medicine  
Here we present CONTIGuator, a software tool for contigs mapping over a reference genome which allows the visualization of a map of contigs, underlining loss and/or gain of genetic elements and permitting  ...  However, a limiting step of genome sequencing is the finishing process, needed to infer the relative position of each contig and close sequencing gaps.  ...  of Yersinia enterocolitica, Roland Siezen for the unassembled contigs of Lactococcus lactis, Matteo Brilli for the critical reading of the manuscript, Marco Fondi and Florent Lassalle for the test sessions  ... 
doi:10.1186/1751-0473-6-11 pmid:21693004 pmcid:PMC3133546 fatcat:zkrtllxqgncnff5gbuvmqhtigy

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  ...  Availability: BamView and Artemis are freely available software. These can be downloaded from their home pages:  ...  used Artemis and Artemis Comparison Tool (ACT), although it can also be used as a portable, standalone, viewer.  ... 
doi:10.1093/bib/bbr073 pmid:22253280 pmcid:PMC3603209 fatcat:kro24phha5hthoyopfyddnpd6i

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.  ...  As a world-leading publisher of scientific, technical and health information, Elsevier is dedicated to linking researchers and professionals to the best thinking in their fields.  ...  Acknowledgements Sequencing of the Plasmodium falciparum genome was supported by the Wellcome Trust, The US National Institutes of Health (NIAID), the Burroughs Wellcome Fund, and the US Department of  ... 
doi:10.1016/j.pt.2004.09.003 pmid:15522662 fatcat:xdwq5sjro5a7pfv4sytnuiqxwy

Fuzzy Logic Control for energy saving in Autonomous Electric Vehicles

A. O. Al-Jazaeri, L. Samaranayake, S. Longo, D. J. Auger
2014 2014 IEEE International Electric Vehicle Conference (IEVC)  
Particle swarm optimization is used in the control design. Comparisons on energy consumption and maximum power demand have been carried out using HIL system for NEDC and ARTEMIS drive cycles.  ...  In this paper, we present a Type-2 Fuzzy Logic Controller (Type-2 FLC) as the speed controller, acting as the Driver Model Controller (DMC) in Autonomous Electric Vehicles (AEV).  ...  ACKNOWLEDGMENT Authors wish to acknowledge the financial support from the "Developing FUTURE Vehicles" research project (EPSRC grant number: EP/I038586/1).  ... 
doi:10.1109/ievc.2014.7056100 fatcat:dgx4owxpdjbpxfkwocu6cy5dz4

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.  ...  Navigating the start of the protein Artemis Program contains a tool which navigates the start of the gene.  ... 
doi:10.5281/zenodo.3600269 fatcat:v2mlweaqlnearino3vmntofmma
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