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1.  SpolPred: rapid and accurate prediction of Mycobacterium tuberculosis spoligotypes from short genomic sequences 
Bioinformatics  2012;28(22):2991-2993.
Summary: Spoligotyping is a well-established genotyping technique based on the presence of unique DNA sequences in Mycobacterium tuberculosis (Mtb), the causal agent of tuberculosis disease (TB). Although advances in sequencing technologies are leading to whole-genome bacterial characterization, tens of thousands of isolates have been spoligotyped, giving a global view of Mtb strain diversity. To bridge the gap, we have developed SpolPred, a software to predict the spoligotype from raw sequence reads. Our approach is compared with experimentally and de novo assembly determined strain types in a set of 44 Mtb isolates. In silico and experimental results are identical for almost all isolates (39/44). However, SpolPred detected five experimentally false spoligotypes and was more accurate and faster than the assembling strategy. Application of SpolPred to an additional seven isolates with no laboratory data led to types that clustered with identical experimental types in a phylogenetic analysis using single-nucleotide polymorphisms. Our results demonstrate the usefulness of the tool and its role in revealing experimental limitations.
Availability and implementation: SpolPred is written in C and is available from www.pathogenseq.org/spolpred.
Contact: francesc.coll@lshtm.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics Online.
doi:10.1093/bioinformatics/bts544
PMCID: PMC3496340  PMID: 23014632
2.  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
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.  Detecting SNPs and estimating allele frequencies in clonal bacterial populations by sequencing pooled DNA 
Bioinformatics  2009;25(16):2074-2075.
Summary: Here, we present a method for estimating the frequencies of SNP alleles present within pooled samples of DNA using high-throughput short-read sequencing. The method was tested on real data from six strains of the highly monomorphic pathogen Salmonella Paratyphi A, sequenced individually and in a pool. A variety of read mapping and quality-weighting procedures were tested to determine the optimal parameters, which afforded ≥80% sensitivity of SNP detection and strong correlation with true SNP frequency at poolwide read depth of 40×, declining only slightly at read depths 20–40×.
Availability: The method was implemented in Perl and relies on the opensource software Maq for read mapping and SNP calling. The Perl script is freely available from ftp://ftp.sanger.ac.uk/pub/pathogens/pools/.
Contact: kh2@sanger.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
doi:10.1093/bioinformatics/btp344
PMCID: PMC2722999  PMID: 19497932
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)