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RefSeq: an update on prokaryotic genome annotation and curation

Daniel H Haft, Michael DiCuccio, Azat Badretdin, Vyacheslav Brover, Vyacheslav Chetvernin, Kathleen O'Neill, Wenjun Li, Farideh Chitsaz, Myra K Derbyshire, Noreen R Gonzales, Marc Gwadz, Fu Lu (+9 others)
2017 Nucleic Acids Research  
Genomes are annotated by a single Prokaryotic Genome Annotation Pipeline (PGAP) to provide users with a resource that is as consistent and accurate as possible.  ...  (HMMs), release of an updated pipeline (PGAP-4), and comprehensive re-annotation of RefSeq prokaryotic genomes.  ...  For bacterial and archaeal genomes, the focus of this article, RefSeq uses a single annotation pipeline, PGAP (Prokaryotic Genome Annotation Pipeline) (3) and generates structural and functional annotation  ... 
doi:10.1093/nar/gkx1068 pmid:29112715 pmcid:PMC5753331 fatcat:hgvzb5wly5flvfsj7wlev6myby

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, Rich McVeigh, Bhanu Rajput, Barbara Robbertse, Brian Smith-White, Danso Ako-Adjei, Alexander Astashyn, Azat Badretdin (+43 others)
2015 Nucleic Acids Research  
The RefSeq project at the National Center for Biotechnology Information (NCBI) maintains and curates a publicly available database of annotated genomic, transcript, and protein sequence records (http:/  ...  This paper summarizes the current status of the viral, prokaryotic, and eukaryotic branches of the RefSeq project, reports on improvements to data access and details efforts to further expand the taxonomic  ...  and accuracy of the represented sequence, structural annotation, and functional annotation.  ... 
doi:10.1093/nar/gkv1189 pmid:26553804 pmcid:PMC4702849 fatcat:2bm7d5coyvfotaj23hnj3mce6m

Solving the Problem: Genome Annotation Standards before the Data Deluge

William Klimke, Claire O'Donovan, Owen White, J. Rodney Brister, Karen Clark, Boris Fedorov, Ilene Mizrachi, Kim D. Pruitt, Tatiana Tatusova
2011 Standards in Genomic Sciences  
The development of a set of minimal standards, including the requirement for annotated complete prokaryotic genomes to contain a full set of ribosomal RNAs, transfer RNAs, and proteins encoding core conserved  ...  prokaryotic genomes are available as gold standard references.  ...  Acknowledgements The authors would like to thank the J.  ... 
doi:10.4056/sigs.2084864 pmid:22180819 pmcid:PMC3236044 fatcat:57nszc6myncm5grcgonmngldl4

Meeting report: a workshop on Best Practices in Genome Annotation

R. Madupu, L. M. Brinkac, J. Harrow, L. G. Wilming, U. Bohme, P. Lamesch, L. I. Hannick
2010 Database: The Journal of Biological Databases and Curation  
Standards and Methods Prokaryotic genome annotation pipeline and standards at the J. Craig Venter Institute Introduction. Dr Ramana Madupu presented JCVI's modular prokaryotic annotation pipeline.  ...  TAIR curators currently do not annotate gene models with 'retained introns' nor do they add non-coding isoforms to protein-coding genes.  ... 
doi:10.1093/database/baq001 pmid:20428316 pmcid:PMC2860899 fatcat:ibdlwzv74veqrb6mzl7nkyr3km

Structural genomics target selection for the New York consortium on membrane protein structure

Marco Punta, James Love, Samuel Handelman, John F. Hunt, Lawrence Shapiro, Wayne A. Hendrickson, Burkhard Rost
2009 Journal of Structural and Functional Genomics  
We first extract all annotated proteins from our reagent genomes, i.e. the 96 fully sequenced prokaryotic genomes from which we clone DNA.  ...  The New York Consortium on Membrane Protein Structure (NYCOMPS), a part of the Protein Structure Initiative (PSI) in the USA, has as its mission to establish a high-throughput pipeline for determination  ...  to Guy Yachdav and Laszlo Kajan (both Columbia) for computer assistance and the collection of genome data sets.  ... 
doi:10.1007/s10969-009-9071-1 pmid:19859826 pmcid:PMC2780672 fatcat:fvxpx3k2jnbsxofcj6hnqalnma

Genome Sequence of the Pea Aphid Acyrthosiphon pisum

Jonathan A. Eisen
2010 PLoS Biology  
Gene family expansions relative to other published genomes include genes involved in chromatin modification, miRNA synthesis, and sugar transport.  ...  Aphids are important agricultural pests and also biological models for studies of insect-plant interactions, symbiosis, virus vectoring, and the developmental causes of extreme phenotypic plasticity.  ...  The members of The International Aphid Genomics Consortium (IAGC) are as follows: Sequencing leadership: Stephen Richards 1 ,  ... 
doi:10.1371/journal.pbio.1000313 pmid:20186266 pmcid:PMC2826372 fatcat:hhcrozfx6ja33f4ko6uq4fpf34

Expanding standards in viromics: in silico evaluation of dsDNA viral genome identification, classification, and auxiliary metabolic gene curation

Akbar Adjie Pratama, Benjamin Bolduc, Ahmed A. Zayed, Zhi-Ping Zhong, Jiarong Guo, Dean R. Vik, Maria Consuelo Gazitúa, James M. Wainaina, Simon Roux, Matthew B. Sullivan
2021 PeerJ  
Conclusion Together, these benchmarking experiments and annotation guidelines should aid researchers seeking to best detect, classify, and characterize the myriad viruses 'hidden' in diverse sequence datasets  ...  Finally, we highlight how fragmented assemblies can lead to erroneous identification of AMGs and outline a best-practices workflow to curate candidate AMGs in viral genomes assembled from metagenomes.  ...  Heather Maughan and Chistine Sun for comments on the structure of an early draft of the manuscript, Drs. Ho Bin Jang and Olivier Zablocki, as well as Mohamed M.  ... 
doi:10.7717/peerj.11447 pmid:34178438 pmcid:PMC8210812 fatcat:xxoxuyekxnfqleia2rfw5mivae

UniProt: a worldwide hub of protein knowledge

2018 Nucleic Acids Research  
Detailed annotations extracted from the literature by expert curators have been collected for over half a million of these proteins.  ...  The UniProt website has been augmented with new data visualizations for the subcellular localization of proteins as well as their structure and interactions.  ...  ACKNOWLEDGEMENTS The UniProt publication has been prepared by Alex Bateman, Maria-Jesus Martin, Sandra Orchard  ... 
doi:10.1093/nar/gky1049 pmid:30395287 fatcat:cixu4a46wnffjed6xuzckik7he

Fungal genome resources at NCBI

B Robbertse, T Tatusova
2011 Mycology  
Searching all databases with Fungi [organism] at http://www.ncbi.nlm.nih.gov/ is the quickest way to find resources of interest with fungal entries.  ...  Gene and BioProject pages also serve as portals to external data such as community annotation websites, BioGrid and UniProt. There are many different ways of accessing genomic data at NCBI.  ...  The Gnomon or multi-genome Gnomon annotation pipeline is computationally intensive, but genomes can be annotated through the pipeline at NCBI by request (genomes@ncbi.nlm.nih.gov).  ... 
doi:10.1080/21501203.2011.584576 pmid:22737589 pmcid:PMC3379888 fatcat:7rqiu7yzhrc4bekzubkk6rfqde

VADR: validation and annotation of virus sequence submissions to GenBank

Alejandro A. Schäffer, Eneida L. Hatcher, Linda Yankie, Lara Shonkwiler, J. Rodney Brister, Ilene Karsch-Mizrachi, Eric P. Nawrocki
2020 BMC Bioinformatics  
The annotation system is based on the analysis of the input nucleotide sequence using models built from curated RefSeqs.  ...  Hidden Markov models are used to classify sequences by determining the RefSeq they are most similar to, and feature annotation from the RefSeq is mapped based on a nucleotide alignment of the full sequence  ...  Acknowledgements We thank Estéban Finol and Mariano Garcia-Blanco for providing predicted RNA structures for the Dengue virus RefSeqs, Alex Kotliarov for incorporating VADR into the GenBank submission  ... 
doi:10.1186/s12859-020-3537-3 pmid:32448124 fatcat:2x3nugbccbfd3a7x5nti245oaq

VADR: validation and annotation of virus sequence submissions to GenBank

Alejandro A Schäffer, Eneida L Hatcher, Linda Yankie, Lara Shonkwiler, J Rodney Brister, Ilene Karsch-Mizrachi, Eric P Nawrocki
2019 biorxiv/medrxiv  
The annotation system is based on the analysis of the input nucleotide sequence using models built from curated RefSeqs.  ...  Predicted proteins encoded by the sequence are validated with nucleotide-to-protein alignments using BLAST.  ...  Acknowledgements We thank Estéban Finol and Mariano Garcia-Blanco for providing predicted RNA structures for the Dengue virus RefSeqs, Alex Kotliarov for incorporating VADR into the GenBank submission  ... 
doi:10.1101/852657 fatcat:xlnfpjevmrgp5bexsm6y4wxj6a

Prokaryotic and Viral Community Composition of Freshwater Springs in Florida, USA

Kema Malki, Karyna Rosario, Natalie A. Sawaya, Anna J. Székely, Michael J. Tisza, Mya Breitbart, Mary Ann Moran
2020 mBio  
Sequencing resulted in the completion of 58 novel viral genomes representing members of the order Caudovirales as well as prokaryotic and eukaryotic single-stranded DNA (ssDNA) viruses.  ...  aquifer system (FAS), to investigate prokaryotic and viral communities from the aquifer.  ...  in the NCBI RefSeq viral database (containing ϳ10,000 curated representative complete viral genomes).  ... 
doi:10.1128/mbio.00436-20 pmid:32265327 fatcat:636bgzj4ffgcjducuqfetwh2hi

Deep sea sediments associated with cold seeps are a subsurface reservoir of viral diversity

Zexin Li, Donald Pan, Guangshan Wei, Weiling Pi, Chuwen Zhang, Jiang-Hai Wang, Yongyi Peng, Lu Zhang, Yong Wang, Casey R J Hubert, Xiyang Dong
2021 The ISME Journal  
Metabolic predictions of prokaryotic host genomes and viral AMGs suggest that viruses influence microbial hydrocarbon biodegradation at cold seeps, as well as other carbon, sulfur and nitrogen cycling  ...  Most cold seep viruses display high degrees of endemism with seep fluid flux being one of the main drivers of viral community composition.  ...  Viral RefSeq (v85) was selected as the reference database, and Diamond was used for the protein-protein similarity method. Other parameters were set as default.  ... 
doi:10.1038/s41396-021-00932-y pmid:33649554 fatcat:6g6div23ojbm5imperhg5jif2i

UniProt: the universal protein knowledgebase in 2021

The UniProt Consortium, Alex Bateman, Maria-Jesus Martin, Sandra Orchard, Michele Magrane, Rahat Agivetova, Shadab Ahmad, Emanuele Alpi, Emily H Bowler-Barnett, Ramona Britto, Borisas Bursteinas, Hema Bye-A-Jee (+122 others)
2020 Nucleic Acids Research  
The aim of the UniProt Knowledgebase is to provide users with a comprehensive, high-quality and freely accessible set of protein sequences annotated with functional information.  ...  We continue to extract detailed annotations from the literature to add to reviewed entries and supplement these in unreviewed entries with annotations provided by automated systems such as the newly implemented  ...  ACKNOWLEDGEMENTS The UniProt publication has been prepared by Alex Bateman, Maria  ... 
doi:10.1093/nar/gkaa1100 pmid:33237286 pmcid:PMC7778908 fatcat:6rwvp6l5uzb3li4lygf2gny6qq

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 Leipe, Richard Mcveigh, Kathleen O'Neill, Barbara Robbertse, Shobha Sharma, Vladimir Soussov (+4 others)
2020 Database: The Journal of Biological Databases and Curation  
This means that relations among data elements can be adjusted in more detail, resulting in expanded annotation of synonyms, the ability to flag names with specific nomenclatural properties, enhanced tracking  ...  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  ...  Acknowledgements The authors were supported by the Intramural Research Program of the National Library of Medicine, National Institutes of Health.  ... 
doi:10.1093/database/baaa062 pmid:32761142 fatcat:bnhdt2p6szf4rb2b2cerhg2bbq
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