NCBI Viral Genomes Resource
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TLDR
The NCBI Viral Genomes Resource is a reference resource designed to bring order to this sequence shockwave and improve usability of viral sequence data.Abstract:
Recent technological innovations have ignited an explosion in virus genome sequencing that promises to fundamentally alter our understanding of viral biology and profoundly impact public health policy. Yet, any potential benefits from the billowing cloud of next generation sequence data hinge upon well implemented reference resources that facilitate the identification of sequences, aid in the assembly of sequence reads and provide reference annotation sources. The NCBI Viral Genomes Resource is a reference resource designed to bring order to this sequence shockwave and improve usability of viral sequence data. The resource can be accessed at http://www.ncbi.nlm.nih.gov/genome/viruses/ and catalogs all publicly available virus genome sequences and curates reference genome sequences. As the number of genome sequences has grown, so too have the difficulties in annotating and maintaining reference sequences. The rapid expansion of the viral sequence universe has forced a recalibration of the data model to better provide extant sequence representation and enhanced reference sequence products to serve the needs of the various viral communities. This, in turn, has placed increased emphasis on leveraging the knowledge of individual scientific communities to identify important viral sequences and develop well annotated reference virus genome sets.read more
Citations
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Journal ArticleDOI
Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation
Nuala A. O'Leary,Mathew W. Wright,J. Rodney Brister,Stacy Ciufo,Diana Haddad,Richard McVeigh,Bhanu Rajput,Barbara Robbertse,Brian Smith-White,Danso Ako-adjei,Alexander Astashyn,Azat Badretdin,Yiming Bao,Olga Blinkova,Vyacheslav Brover,Vyacheslav Chetvernin,Jinna Choi,Eric Cox,Olga Ermolaeva,Catherine M. Farrell,Tamara Goldfarb,Tripti Gupta,Daniel H. Haft,Eneida L. Hatcher,Wratko Hlavina,Vinita Joardar,Vamsi K. Kodali,Wenjun Li,Donna Maglott,Patrick Masterson,Kelly M. McGarvey,Michael R. Murphy,Kathleen O'Neill,Shashikant Pujar,Sanjida H. Rangwala,Daniel Rausch,Lillian D. Riddick,Conrad L. Schoch,Andrei Shkeda,Susan S. Storz,Hanzhen Sun,Françoise Thibaud-Nissen,Igor Tolstoy,Raymond E. Tully,Anjana R. Vatsan,Craig Wallin,David Webb,Wendy Wu,Melissa J. Landrum,Avi Kimchi,Tatiana Tatusova,Michael DiCuccio,Paul Kitts,Terence Murphy,Kim D. Pruitt +54 more
TL;DR: The approach to utilizing available RNA-Seq and other data types in the authors' manual curation process for vertebrate, plant, and other species is summarized, and a new direction for prokaryotic genomes and protein name management is described.
Journal ArticleDOI
BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes.
Mosè Manni,Mosè Manni,Matthew R Berkeley,Matthew R Berkeley,Mathieu Seppey,Mathieu Seppey,Felipe A. Simão,Felipe A. Simão,Evgeny M. Zdobnov,Evgeny M. Zdobnov +9 more
TL;DR: New functionalities and major improvements of the BUSCO software are presented, as well as the renewal and expansion of the underlying datasets in sync with the OrthoDB v10 release.
Journal ArticleDOI
Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle.
Edoardo Pasolli,Francesco Asnicar,Serena Manara,Moreno Zolfo,Nicolai Karcher,Federica Armanini,Francesco Beghini,Paolo Manghi,Adrian Tett,Paolo Ghensi,Maria Carmen Collado,Benjamin L. Rice,Casey DuLong,Xochitl C. Morgan,Christopher D. Golden,Christopher Quince,Curtis Huttenhower,Nicola Segata +17 more
TL;DR: Thousands of microbial genomes from yet-to-be-named species are identified, the pangenomes of human-associated microbes are expanded, and better exploitation of metagenomic technologies are allowed.
Journal ArticleDOI
NCBI Taxonomy: a comprehensive update on curation, resources and tools.
Conrad L. Schoch,Stacy Ciufo,Mikhail Domrachev,Carol L. Hotton,Sivakumar Kannan,Rogneda Khovanskaya,Detlef D. Leipe,Richard McVeigh,Kathleen O'Neill,Barbara Robbertse,Shobha Sharma,Vladimir Soussov,John P. Sullivan,Lu Sun,Seán Turner,Ilene Karsch-Mizrachi +15 more
TL;DR: The National Center for Biotechnology Information (NCBI) Taxonomy includes organism names and classifications for every sequence in the nucleotide and protein sequence databases of the International Nucleotide Sequence Database Collaboration.
Journal Article
Database resources of the national center for biotechnology information and its application
TL;DR: The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank® nucleic acid sequence database and the PubMed database of citations and abstracts for published life science journals.
References
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Database resources of the National Center for Biotechnology Information
David L. Wheeler,Deanna M. Church,Ron Edgar,Scott Federhen,Wolfgang Helmberg,Thomas L. Madden,Joan Pontius,Gregory D. Schuler,Lynn M. Schriml,Edwin Sequeira,Tugba O. Suzek,Tatiana Tatusova,Lukas Wagner +12 more
TL;DR: In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI’s website.
Journal ArticleDOI
NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins
TL;DR: The National Center for Biotechnology Information Reference Sequence (RefSeq) database provides a non-redundant collection of sequences representing genomic data, transcripts and proteins that pragmatically includes sequence data that are currently publicly available in the archival databases.
Journal ArticleDOI
NCBI BLAST: a better web interface
Mark D. Johnson,Irena Zaretskaya,Yan Raytselis,Yuri Merezhuk,Scott D. McGinnis,Thomas L. Madden +5 more
TL;DR: The public interface of BLAST at the NCBI website has recently been reengineered to improve usability and performance, and key new features include simplified search forms, improved navigation, and a list of recent BLAST results.
Book
Virus taxonomy: classification and nomenclature of viruses. Seventh report of the International Committee on Taxonomy of Viruses.
TL;DR: This report builds on the accumulated taxonomic construction of the eight previous reports dating back to 1971 and records the proceedings of the Committee since publication of the last report in 2005.
Journal ArticleDOI
Consensus proposals for a unified system of nomenclature of hepatitis C virus genotypes.
Peter Simmonds,Jens Bukh,Christophe Combet,Gilbert Deléage,Nobuyuki Enomoto,Stephen M. Feinstone,Phillippe Halfon,Geneviève Inchauspé,Carla Kuiken,Geert Maertens,Masashi Mizokami,Donald G. Murphy,Hiroaki Okamoto,Jean-Michel Pawlotsky,François Penin,Erwin Sablon,Tadasu Shin-I,Lieven Stuyver,Heinz-Jürgen Thiel,Sergei Viazov,Amy J. Weiner,Anders Widell +21 more
TL;DR: These proposals provide the framework by which the HCV databases store and provide access to data on HCV, which will internationally coordinate the assignment of new genotypes and subtypes in the future.