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Artemis: sequence visualization and annotation

K. Rutherford, J. Parkhill, J. Crook, T. Horsnell, P. Rice, M.-A. Rajandream, B. Barrell
2000 Bioinformatics  
Artemis is a DNA sequence visualization and annotation tool that allows the results of any analysis or sets of analyses to be viewed in the context of the sequence and its six-frame translation.  ...  It is implemented in Java, and can be run on any suitable platform. Sequences and annotation can be read and  ...  Acknowledgements The development of Artemis was funded by the Wellcome Trust's Beowulf Genomics initiative through its support of the Sanger Centre Pathogen Sequencing Unit.  ... 
doi:10.1093/bioinformatics/16.10.944 pmid:11120685 fatcat:pbxox3xrybg3tiu4p452qporei

HBVRegDB: Annotation, comparison, detection and visualization of regulatory elements in hepatitis B virus sequences

Nattanan Panjaworayan, Stephan K Roessner, Andrew E Firth, Chris M Brown
2007 Virology Journal  
The many Hepadnaviridae sequences available have widely varied functional annotation.  ...  In addition to INSDC and RefSeq annotation, HBVRegDB also contains expert and systematically calculated annotations (e.g. promoters) and comparative genome analysis results (e.g. blastn, tblastx).  ...  This alignment is The highly annotated reference sequence (AM282986) in Genbank format visualized by VectorNTI Figure 2 The highly annotated reference sequence (AM282986) in Genbank format visualized  ... 
doi:10.1186/1743-422x-4-136 pmid:18086305 pmcid:PMC2235840 fatcat:5gzlzwthqzeq5ck53c4mdgjmvm

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  
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  ...  Genome sequences, annotation and pre-computed comparisons are stored in a relational database allowing flexible querying based on userdefined sequence regions, from whole genome to a defined region flanking  ...  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

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:  ...  ., 2010) is a genome and annotation visualization and analysis tool.  ... 
doi:10.1093/bioinformatics/btr703 pmid:22199388 pmcid:PMC3278759 fatcat:57t7vj3jn5c2rcb3uliyxjxnxy

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.  ...  Therefore, a new version of Artemis has been developed, which reads from and writes to a relational database schema, and allows users to annotate more complex, often large and fragmented, genome sequences  ...  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: Attention-based Retrieval with Text-Explicit Matching and Implicit Similarity [article]

Ginger Delmas and Rafael Sampaio de Rezende and Gabriela Csurka and Diane Larlus
2022 arXiv   pre-print
Our work aims at shedding new light on the task by looking at it through the prism of two familiar and related frameworks: text-to-image and image-to-image retrieval.  ...  An intuitive way to search for images is to use queries composed of an example image and a complementary text.  ...  Let φ(.) and θ(.) be the visual and textual encoders respectively.  ... 
arXiv:2203.08101v2 fatcat:uwqqwuwazvbl7ajowvdj4uknze

Artemis: Articulated Neural Pets with Appearance and Motion synthesis [article]

Haimin Luo, Teng Xu, Yuheng Jiang, Chenglin Zhou, Qiwei Qiu, Yingliang Zhang, Wei Yang, Lan Xu, Jingyi Yu
2022 arXiv   pre-print
We make available our ARTEMIS model and dynamic furry animal dataset at https://haiminluo.github.io/publication/artemis/.  ...  In this paper, we present ARTEMIS, a novel neural modeling and rendering pipeline for generating ARTiculated neural pets with appEarance and Motion synthesIS.  ...  This work was supported by NSFC programs (61976138, 61977047), the National Key Research and Development Program (2018YFB2100 500), STCSM (2015F0203-000-06) and SHMEC (2019-01-07-00-01-E00003).  ... 
arXiv:2202.05628v2 fatcat:v7f6tg64fvfohmtl7riiecn5fu

DIANA-miTED: a microRNA tissue expression database

Ioannis Kavakiotis, Athanasios Alexiou, Spyros Tastsoglou, Ioannis S Vlachos, Artemis G Hatzigeorgiou
2021 Nucleic Acids Research  
tissues, 82 anatomical sublocations, 267 cell lines and 261 diseases. miTED offers rich instant visualizations of the expression and sample distributions of requested data across variables, as well as  ...  DIANA-miTED is the most comprehensive and systematic collection of miRNA expression values derived from the analysis of 15 183 raw human small RNA-Seq (sRNA-Seq) datasets from the Sequence Read Archive  ...  ACKNOWLEDGEMENTS The results published here are in part based upon data generated by The Cancer Genome Atlas managed by the NCI and NHGRI.  ... 
doi:10.1093/nar/gkab733 pmid:34469540 pmcid:PMC8728140 fatcat:nkkukmo445hhjej2rmbo6wnmta

Visual Goal-Step Inference using wikiHow [article]

Yue Yang, Artemis Panagopoulou, Qing Lyu, Li Zhang, Mark Yatskar, Chris Callison-Burch
2021 arXiv   pre-print
We propose the Visual Goal-Step Inference (VGSI) task, where a model is given a textual goal and must choose which of four images represents a plausible step towards that goal.  ...  We introduce the visual analogue.  ...  We thank Chenyu Liu for annotations. We also thank Simmi Mourya, Keren Fuentes, Carl Vondrick, Zsolt Kira, Mohit Bansal, Lara Martin, and anonymous reviewers for their valuable feedback.  ... 
arXiv:2104.05845v2 fatcat:nsli5d55zza3hjsyeih2j3aili

A novel emaravirus identified in maple with leaf mottle symptoms by deep sequencing [article]

Artemis Rumbou, Thierry Candresse, Susanne von Bargen, Carmen Buettner
2020 bioRxiv   pre-print
sequence data was generated.  ...  Purified double-stranded cDNA from each sample were used for RNA-Seq analysis on the Illumina HiSeq2500system and 14-198 MB data/sample of 100 bp-long paired-end sequence reads were generated.  ...  The taxonomic content of the obtained datasets, as provided by the BLAST 164 annotations, was visualized using MEGAN (Huson et al., 2016) , in which the BLAST 165 results were parsed to assign the best  ... 
doi:10.1101/2020.10.05.325928 fatcat:o6ojni4hkza4pl7h2agtppt4wa

DIANA-miRPath v3.0: deciphering microRNA function with experimental support

Ioannis S. Vlachos, Konstantinos Zagganas, Maria D. Paraskevopoulou, Georgios Georgakilas, Dimitra Karagkouni, Thanasis Vergoulis, Theodore Dalamagas, Artemis G. Hatzigeorgiou
2015 Nucleic Acids Research  
The new miRPath web server renders possible the functional annotation of one or more miRNAs using standard (hypergeometric distributions), unbiased empirical distributions and/or meta-analysis statistics  ...  A unique feature of DIANA-miRPath v3.0 is its redesigned Reverse Search module, which enables users to identify and visualize miRNAs significantly controlling selected pathways or belonging to specific  ...  User interface, results presentation and visualizations.  ... 
doi:10.1093/nar/gkv403 pmid:25977294 pmcid:PMC4489228 fatcat:thu67ur6qjb3xncaavr226lq2m

Solving the transcription start site identification problem with ADAPT-CAGE: a Machine Learning algorithm for analysis of CAGE data [article]

Georgios K Georgakilas, Nikos Perdikopanis, Artemis Hatzigeorgiou
2019 bioRxiv   pre-print
It has been specifically designed aiming for flexibility and ease-of-use by only requiring aligned CAGE data and the underlying genomic sequence.  ...  ADAPT-CAGE provides annotation-agnostic, highly accurate and single-nucleotide resolution experimentally derived TSSs on a genome-wide scale.  ...  Normalized signal profiles were also added as a visual aid.  ... 
doi:10.1101/752253 fatcat:gplqrctqlrc2nmwj3uelwb36fy

Event detection in video using motion analysis

Ricardo Castellanos, Hari Kalva, Oge Marques, Borko Furht
2010 Proceedings of the first ACM international workshop on Analysis and retrieval of tracked events and motion in imagery streams - ARTEMIS '10  
The main objective of this work is the analysis of computer vision techniques and algorithms to perform automatic detection of specific events in video sequences.  ...  Large amount of video in surveillance and security requires systems capable of processing video to automatically detect and recognize events to alleviate the load on humans and enable preventive actions  ...  Multimedia data such as video sequences in visual surveillance systems is a very important topic and probably one of the most illustrative examples of this challenge because the large demand for analysis  ... 
doi:10.1145/1877868.1877884 dblp:conf/mm/CastellanosKMF10 fatcat:anzw4czpnfch7anusmu3ve2xg4

AGAMEMNON: an Accurate metaGenomics And MEtatranscriptoMics quaNtificatiON analysis suite

Giorgos Skoufos, Fatemeh Almodaresi, Mohsen Zakeri, Joseph N. Paulson, Rob Patro, Artemis G. Hatzigeorgiou, Ioannis S. Vlachos
2022 Genome Biology  
AGAMEMNON provides an R-Shiny application, permitting performance of investigations and visualizations from a graphics interface.  ...  , or sequenced host samples.  ...  Peer review information Kevin Pang was the primary editor of this article and managed its editorial process and peer review in collaboration with the rest of the editorial team.  ... 
doi:10.1186/s13059-022-02610-4 pmid:35101114 pmcid:PMC8802518 fatcat:wutwajg2gbex7ot62wuz26zc34
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