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1.  Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data 
Bioinformatics  2011;28(4):464-469.
Motivation: High-throughput sequencing (HTS) technologies have made low-cost sequencing of large numbers of samples commonplace. An explosion in the type, not just number, of sequencing experiments has also taken place including genome re-sequencing, population-scale variation detection, whole transcriptome sequencing and genome-wide analysis of protein-bound nucleic acids.
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: http://www.sanger.ac.uk/resources/software/artemis/.
Contact: artemis@sanger.ac.uk; tjc@sanger.ac.uk
doi:10.1093/bioinformatics/btr703
PMCID: PMC3278759  PMID: 22199388
2.  Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology 
Bioinformatics  2010;26(14):1704-1707.
Motivation: The accuracy of reference genomes is important for downstream analysis but a low error rate requires expensive manual interrogation of the sequence. Here, we describe a novel algorithm (Iterative Correction of Reference Nucleotides) that iteratively aligns deep coverage of short sequencing reads to correct errors in reference genome sequences and evaluate their accuracy.
Results: Using Plasmodium falciparum (81% A + T content) as an extreme example, we show that the algorithm is highly accurate and corrects over 2000 errors in the reference sequence. We give examples of its application to numerous other eukaryotic and prokaryotic genomes and suggest additional applications.
Availability: The software is available at http://icorn.sourceforge.net
Contact: tdo@sanger.ac.uk; cnewbold@hammer.imm.ox.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
doi:10.1093/bioinformatics/btq269
PMCID: PMC2894513  PMID: 20562415
3.  BamView: viewing mapped read alignment data in the context of the reference sequence 
Bioinformatics  2010;26(5):676-677.
Summary: BamView is an interactive Java application for visualizing the large amounts of data stored for sequence reads which are aligned against a reference genome sequence. It supports the BAM (Binary Alignment/Map) format. It can be used in a number of contexts including SNP calling and structural annotation. BamView has also been integrated into Artemis so that the reads can be viewed in the context of the nucleotide sequence and genomic features.
Availability: BamView and Artemis are freely available (under a GPL licence) for download (for MacOSX, UNIX and Windows) at: http://bamview.sourceforge.net/
Contact: artemis@sanger.ac.uk
doi:10.1093/bioinformatics/btq010
PMCID: PMC2828118  PMID: 20071372
4.  ABACAS: algorithm-based automatic contiguation of assembled sequences 
Bioinformatics  2009;25(15):1968-1969.
Summary: Due to the availability of new sequencing technologies, we are now increasingly interested in sequencing closely related strains of existing finished genomes. Recently a number of de novo and mapping-based assemblers have been developed to produce high quality draft genomes from new sequencing technology reads. New tools are necessary to take contigs from a draft assembly through to a fully contiguated genome sequence. ABACAS is intended as a tool to rapidly contiguate (align, order, orientate), visualize and design primers to close gaps on shotgun assembled contigs based on a reference sequence. The input to ABACAS is a set of contigs which will be aligned to the reference genome, ordered and orientated, visualized in the ACT comparative browser, and optimal primer sequences are automatically generated.
Availability and Implementation: ABACAS is implemented in Perl and is freely available for download from http://abacas.sourceforge.net
Contact: sa4@sanger.ac.uk
doi:10.1093/bioinformatics/btp347
PMCID: PMC2712343  PMID: 19497936
5.  Artemis and ACT: Viewing, annotating and comparing sequences stored in a relational database 
Bioinformatics (Oxford, England)  2008;24(23):2672-2676.
Motivation
Artemis and 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 biologists and professional annotators. Nevertheless, its utility has been somewhat restricted by its limitation to reading and writing from flat files. 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
Results
Artemis and ACT have now been extended to read and write directly to the Generic Model Organism Database (GMOD, http://www.gmod.org) Chado relational database schema. In addition, a Gene Builder tool has been developed to provide structured forms and tables to edit coordinates of gene models and edit functional annotation, based on standard ontologies, controlled vocabularies and free text.
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:
http://www.sanger.ac.uk/Software/Artemis/
http://www.sanger.ac.uk/Software/ACT/
doi:10.1093/bioinformatics/btn529
PMCID: PMC2606163  PMID: 18845581
6.  DNAPlotter: Circular and linear interactive genome visualisation 
Bioinformatics (Oxford, England)  2008;25(1):119-120.
Summary
DNAPlotter is an interactive Java application for generating circular and linear representations of genomes. Making use of the Artemis libraries to provide a user-friendly method of loading in sequence files (EMBL, GenBank, GFF) as well as data from relational databases, it filters features of interest to display on separate user-definable tracks. It can be used to produce publication quality images for papers or web pages.
Availability
DNAPlotter is freely available (under a GPL licence) for download (for MacOSX, UNIX and Windows) at the Wellcome Trust Sanger Institute web sites:
http://www.sanger.ac.uk/Software/Artemis/circular/
Contact
artemis@sanger.ac.uk
doi:10.1093/bioinformatics/btn578
PMCID: PMC2612626  PMID: 18990721
7.  DNAPlotter: circular and linear interactive genome visualization 
Bioinformatics  2008;25(1):119-120.
Summary: DNAPlotter is an interactive Java application for generating circular and linear representations of genomes. Making use of the Artemis libraries to provide a user-friendly method of loading in sequence files (EMBL, GenBank, GFF) as well as data from relational databases, it filters features of interest to display on separate user-definable tracks. It can be used to produce publication quality images for papers or web pages.
Availability: DNAPlotter is freely available (under a GPL licence) for download (for MacOSX, UNIX and Windows) at the Wellcome Trust Sanger Institute web sites: http://www.sanger.ac.uk/Software/Artemis/circular/
Contact: artemis@sanger.ac.uk
doi:10.1093/bioinformatics/btn578
PMCID: PMC2612626  PMID: 18990721
8.  Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database 
Bioinformatics  2008;24(23):2672-2676.
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 biologists and professional annotators. Nevertheless, its utility has been somewhat restricted by its limitation to reading and writing from flat files. 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.
Results: Artemis and ACT have now been extended to read and write directly to the Generic Model Organism Database (GMOD, http://www.gmod.org) Chado relational database schema. In addition, a Gene Builder tool has been developed to provide structured forms and tables to edit coordinates of gene models and edit functional annotation, based on standard ontologies, controlled vocabularies and free text.
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: http://www.sanger.ac.uk/Software/Artemis/ http://www.sanger.ac.uk/Software/ACT/
Contact: artemis@sanger.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
doi:10.1093/bioinformatics/btn529
PMCID: PMC2606163  PMID: 18845581

Results 1-8 (8)