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Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database
2008
Computer applications in the biosciences : CABIOS
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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
WebACT--an online companion for the Artemis Comparison Tool
2005
Bioinformatics
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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 ...
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
PlasmiR: A Manual Collection of Circulating microRNAs of Prognostic and Diagnostic Value
2021
Cancers
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Our circulating miRNA biomarker collection is provided as an online database, plasmiR. It consists of 1021 entries regarding 251 miRNAs and 112 diseases. ...
Only recently, microRNAs (miRNAs) were found to exist in traceable and distinctive amounts in the human circulatory system, bringing forth the intriguing possibility of using them as minimally invasive ...
Acknowledgments: We gratefully acknowledge the support and feedback from past and present DIANA-Lab members, as well as systems administration support from Athanasios Fevgas and Nikolaos Frangogiannis ...
doi:10.3390/cancers13153680
fatcat:f4nc6ba3xveovogrxxgviespom
Meeting report: a workshop on Best Practices in Genome Annotation
2010
Database: The Journal of Biological Databases and Curation
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Manual annotation data is stored in a separate MySQL database. ...
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
ASAP: a resource for annotating, curating, comparing, and disseminating genomic data
2006
Nucleic Acids Research
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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
ABACAS: algorithm-based automatic contiguation of assembled sequences
2009
Bioinformatics
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ACT: viewing, annotation and comparing sequences stored in relational database. ...
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 ...
doi:10.1093/bioinformatics/btp347
pmid:19497936
pmcid:PMC2712343
fatcat:q3bqwp77zfburlp6sxed32uap4
GenColors: accelerated comparative analysis and annotation of prokaryotic genomes at various stages of completeness
2005
Bioinformatics
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GenColors is a new web-based software/database system aimed at an improved and accelerated annotation of prokaryotic genomes, considering information on related genomes and making extensive use of genome ...
It offers a seamless integration of data from ongoing sequencing projects and annotated genomic sequences obtained from GenBank. ...
The help provided by Kerstin Wagner in setting up and maintaning the SGB external link page as well as in icon design is gratefully acknowledged. ...
doi:10.1093/bioinformatics/bti606
pmid:16076887
fatcat:ldgxvo7qlfb6thqkffuqx6pvl4
coliBASE: an online database for Escherichia coli, Shigella and Salmonella comparative genomics
2004
Nucleic Acids Research
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The data are stored in a relational database, accessible by a number of user-friendly search methods and graphical browsers. ...
We have constructed coliBASE, a database for Escherichia coli, Shigella and Salmonella comparative genomics available online at http://colibase. bham.ac.uk. ...
://ecoli.bham.ac.uk) through a collaboration with Gavin Thomas (University of York). ...
doi:10.1093/nar/gkh031
pmid:14681417
pmcid:PMC308765
fatcat:5hbemym3ubhnlg3jkf3wwy36y4
Annotation, comparison and databases for hundreds of bacterial genomes
2007
Research in Microbiology
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and loops in closely related bacterial genomes ACT http://www.sanger.ac.uk/Software/ACT/ Comparative genome analysis and visualization tools for multiple genome alignments CGAT Research in Microbiology ...
This paper reviews advances in the development of bacterial annotation and comparative analysis tools, and progress in the design of novel database structures for the integration of heterogeneous biological ...
the quality of the primary resources, i.e. the annotation already stored in the databases, and on the quality of the sequence itself. ...
doi:10.1016/j.resmic.2007.09.009
pmid:18031997
fatcat:bfw4zslyw5bgrdtrxhozk2uc7e
Genome Annotation and Comparative Genomics of ORF Virus
2014
Advances in microbiology
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The novel vaccine will have a significant role in the economy of a country through the control of disease in an economically important and small ruminant caused by ORFV. ...
Comparative genomic analysis reveals significant differences in Bovine Papular Stomatitis Virus (BPSV) strain BV-AR02 and ORFV strain OV-SA00, and these may account for differences in host range. ...
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
2011
BMC Research Notes
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A summary of the features of the compared genome browsers is presented and discussed. ...
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. ...
Guerin and S. Sidibé-Bocs for helpful discussions. ...
doi:10.1186/1756-0500-4-133
pmid:21542900
pmcid:PMC3096945
fatcat:nuvzllunibcphph5c6fauebsvq
SynBrowse: a synteny browser for comparative sequence analysis
2005
Bioinformatics
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Each database stores pre-computed alignments from a focus sequence to reference sequences in addition to the genome annotations of the focus sequence. ...
The user interface lets end users select a key comparative alignment type and search for syntenic blocks between two sequences and zoom in to view the relationships among the corresponding genome annotations ...
This work was supported in part by ARS-USDA funds via a subcontract from the National Center for Genome Resources to V.B. ...
doi:10.1093/bioinformatics/bti555
pmid:15994196
fatcat:62gqmzsovfbmtoqvg6sk4a6c3y
inGeno--an integrated genome and ortholog viewer for improved genome to genome comparisons
2006
BMC Bioinformatics
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As shown in this study, inGeno can be applied to study and compare in particular prokaryotic genomes against each other (gram positive and negative as well as close and more distantly related species) ...
annotations and features. ...
Acknowledgements We thank DFG (SFB 688-A2; TR 34-A5) and BMBF for support (PathoG-enoMik 0313134). ...
doi:10.1186/1471-2105-7-461
pmid:17054788
pmcid:PMC1635569
fatcat:pxaovd3ygnhkdnjb7vga3sb52m
MuGeN: simultaneous exploration of multiple genomes and computer analysis results
2003
Bioinformatics
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It is capable of retrieving annotated sequences in several formats, stored in local files, or available in databases over the network. ...
Motivation: The availability of increasing amounts of sequence data about completely sequenced genomes spurs the development of new methods in the fields of automated annotation, and of comparative genomics ...
Both sequence and annotation information are contained in text files well adapted to detailed examination of specific sequence features but ill-suited to rapidly compare two or more entries or to give ...
doi:10.1093/bioinformatics/btg101
pmid:12724296
fatcat:axid74yjgbghveqyyh4jvueq3m
From Sequence Mapping to Genome Assemblies
[chapter]
2014
Msphere
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In this chapter, we fi rst discuss some limitations of the mapping process and how these may be overcome through local sequence assembly. ...
two ways: sequence reads are either mapped to an existing reference sequence, or they are built into a new sequence ("de novo assembly"). ...
Acknowledgements I would like to thank Adam Reid, Martin Hunt, and Bernardo Foth for proofreading the chapter. ...
doi:10.1007/978-1-4939-1438-8_2
pmid:25388106
fatcat:dobmztvzlbctbf6yjz24cshake
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