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RefSeq: an update on prokaryotic genome annotation and curation
2017
Nucleic Acids Research
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(HMMs), release of an updated pipeline (PGAP-4), and comprehensive re-annotation of RefSeq prokaryotic genomes. ...
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. ...
sequence regions (CDS) annotated on RefSeq genomes. ...
doi:10.1093/nar/gkx1068
pmid:29112715
pmcid:PMC5753331
fatcat:hgvzb5wly5flvfsj7wlev6myby
EcoGene-RefSeq: EcoGene tools applied to the RefSeq prokaryotic genomes
2013
Bioinformatics
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EcoGene is a major source of annotation updates for the MG1655 Genbank record, one of only a few Genbank genome records that are updated by a community effort. ...
EcoGene-RefSeq is being developed as a stand-alone internet resource to facilitate the usage of EcoGene-based tools on any of the 42400 completed prokaryotic genome records that are currently available ...
In the future, we can add capabilities into EcoGene-RefSeq, including manual curation tools enabling an individual or interested group to build and re-annotate an EcoGene-like database for any prokaryotic ...
doi:10.1093/bioinformatics/btt302
pmid:23736533
pmcid:PMC3712216
fatcat:jon55wz7lbcoporxe3hb2u2emu
Update on RefSeq microbial genomes resources
2014
Nucleic Acids Research
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A number of improvements have been incorporated into the Prokaryotic Genome Annotation Pipeline. ...
Several new features have been added to RefSeq prokaryotic genomes data processing pipeline including the calculation of genome groups (clades) and the optimization of protein clusters generation using ...
All RefSeq genomes are annotated by NCBI pipeline except for the Reference genomes manually curated by community and NCBI staff (2). ...
doi:10.1093/nar/gku1062
pmid:25510495
pmcid:PMC4383903
fatcat:52oqwfkoircovp4jgymgm4nhry
RefSeq microbial genomes database: new representation and annotation strategy
2013
Nucleic Acids Research
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New strategies have been developed for the annotation and representation of reference genomes and sequence variations derived from population studies and clinical outbreaks. ...
This huge increase in DNA sequence data presents new challenges for the annotation, analysis and visualization bioinformatics tools. ...
RefSeq prokaryotic genomes are organized in several new categories based on curated attributes and assembly and annotation quality measures. ...
doi:10.1093/nar/gkt1274
pmid:24316578
pmcid:PMC3965038
fatcat:7yynuxostnhpjlx6mcrezaekqq
RefSeq microbial genomes database: new representation and annotation strategy
2015
Nucleic Acids Research
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New strategies have been developed for the annotation and representation of reference genomes and sequence variations derived from population studies and clinical outbreaks. ...
This huge increase in DNA sequence data presents new challenges for the annotation, analysis and visualization bioinformatics tools. ...
RefSeq prokaryotic genomes are organized in several new categories based on curated attributes and assembly and annotation quality measures. ...
doi:10.1093/nar/gkv278
pmid:25824943
pmcid:PMC4402550
fatcat:o3opkwpazfdvrkml2uliuxy2py
Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation
2015
Nucleic Acids Research
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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:/ ...
We also highlight diverse functional curation initiatives that support multiple uses of RefSeq data including taxonomic validation, genome annotation, comparative genomics, and clinical testing. ...
and accuracy of the represented sequence, structural annotation, and functional annotation. ...
doi:10.1093/nar/gkv1189
pmid:26553804
pmcid:PMC4702849
fatcat:2bm7d5coyvfotaj23hnj3mce6m
NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy
2011
Nucleic Acids Research
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We report here on recent growth, the status of curating the human RefSeq data set, more extensive feature annotation and current policy for eukaryotic genome annotation via the NCBI annotation pipeline ...
The database includes over 16 000 organisms, 2.4 Â 10 6 genomic records, 13 Â 10 6 proteins and 2 Â 10 6 RNA records spanning prokaryotes, eukaryotes and viruses (RefSeq release 49, September 2011). ...
RefSeq genome representation for prokaryotes is currently managed by propagating annotation from the primary genome data in GenBank, calculating annotation for RefSeq when annotation is not available in ...
doi:10.1093/nar/gkr1079
pmid:22121212
pmcid:PMC3245008
fatcat:n2exzcnlwbfi7ef24fcdeyuaca
NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins
2004
Nucleic Acids Research
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from the scientific community, automated annotation, propagation from GenBank and curation by NCBI staff. ...
The database incorporates data from over 2400 organisms and includes over one million proteins representing significant taxonomic diversity spanning prokaryotes, eukaryotes and viruses. ...
The collection is curated on an ongoing basis by collaborating groups and by NCBI staff. Sequence records are presented in a standard format and are subject to computational validation. ...
doi:10.1093/nar/gki025
pmid:15608248
pmcid:PMC539979
fatcat:gneoq6nakbeptfwoymdt4kfj4e
RefSeq curation and annotation of stop codon recoding in vertebrates
2018
Nucleic Acids Research
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Gene annotations were curated in nine vertebrate model organisms and integrated into NCBI's Reference Sequence (RefSeq) dataset, resulting in 247 selenoprotein genes encoding 322 selenoproteins, and 93 ...
Our goal was to provide accurately curated and annotated datasets of selenoprotein and SCR transcript and protein records to serve as annotation standards and to promote basic and biomedical research. ...
ACKNOWLEDGEMENTS We would like to acknowledge RefSeq curators Catherine Farrell and David Webb, and developers Vamsi Kodali and Alexander Souvorov for helpful consults. ...
doi:10.1093/nar/gky1234
pmid:30535227
pmcid:PMC6344875
fatcat:7uo7isrv7rfnji4nwlwhhrspme
NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins
2007
Nucleic Acids Research
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The format of all RefSeq records is validated, and an increasing number of tests are being applied to evaluate the quality of sequence and annotation, especially in the context of complete genomic sequence ...
NCBI's reference sequence (RefSeq) database (http://www.ncbi.nlm.nih.gov/RefSeq/) is a curated non-redundant collection of sequences representing genomes, transcripts and proteins. ...
gene annotations on the human and mouse genomes. ...
doi:10.1093/nar/gkl842
pmid:17130148
pmcid:PMC1716718
fatcat:t7rciayrzncfnmxhdp44hjk76a
NCBI Reference Sequences: current status, policy and new initiatives
2009
Nucleic Acids Research
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NCBI's Reference Sequence (RefSeq) database (http://www.ncbi.nlm.nih.gov/RefSeq/) is a curated non-redundant collection of sequences representing genomes, transcripts and proteins. ...
We report here on the recent growth of the database, recent changes to feature annotations and record types for eukaryotic (primarily vertebrate) species and policies regarding species inclusion and genome ...
NCBI's computational genome annotation pipelines are used to annotate some prokaryotic and eukaryotic genomes. ...
doi:10.1093/nar/gkn721
pmid:18927115
pmcid:PMC2686572
fatcat:77xptvs54fghxb3dur3ykwycgq
NCBI prokaryotic genome annotation pipeline
2016
Nucleic Acids Research
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The pipeline provides a framework for generation and analysis of annotation on the full breadth of prokaryotic taxonomy. ...
Thus, the new NCBI's Prokaryotic Genome Annotation Pipeline (PGAP) relies more on sequence similarity when confident comparative data are available, while it relies more on statistical predictions in the ...
ACKNOWLEDGEMENTS The authors would like to thank Dr David Lipman for many fruitful discussions about prokaryotic biology, insightful suggestions on improving the annotation results and his continuous support ...
doi:10.1093/nar/gkw569
pmid:27342282
pmcid:PMC5001611
fatcat:6wcveeu35bcixgypu5i2nmnbba
The National Center for Biotechnology Information's Protein Clusters Database
2008
Nucleic Acids Research
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There are 7180 clusters containing 376 513 proteins with curated gene and protein functional annotation. ...
ProtClustDB provides an efficient method to aggregate gene and protein annotation for researchers and is available at http://www.ncbi.nlm.nih.gov/ sites/entrez?db=proteinclusters. ...
It was realized that annotating protein families as a group was a convenient and efficient way to functionally annotate the increasing numbers of prokaryotic genomes that were being deposited at an increasing ...
doi:10.1093/nar/gkn734
pmid:18940865
pmcid:PMC2686591
fatcat:rtrzuma6ubb33i6gsivhsi7yca
Solving the Problem: Genome Annotation Standards before the Data Deluge
2011
Standards in Genomic Sciences
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Standards in Genomic Sciences Table 1 (cont.) Databases, tools,resources for genomes and annotation. ...
prokaryotic genomes are available as gold standard references. ...
Craig Venter Institute for hosting the workshop and especially Tanja Davidsen and Ramana Madupu for help in the organization before, during, and after the workshop. ...
doi:10.4056/sigs.2084864
pmid:22180819
pmcid:PMC3236044
fatcat:57nszc6myncm5grcgonmngldl4
The MACADAM database: a MetAboliC pAthways DAtabase for Microbial taxonomic groups for mining potential metabolic capacities of archaeal and bacterial taxonomic groups
2019
Database: The Journal of Biological Databases and Curation
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For each prokaryotic 'RefSeq complete genome', MACADAM builds a pathway genome database (PGDB) using Pathway Tools software based on MetaCyc data that includes metabolic pathways as well as associated ...
To ensure the highest quality of the genome functional annotation data, MACADAM also contains MicroCyc, a manually curated collection of PGDBs; Functional Annotation of Prokaryotic Taxa (FAPROTAX), a manually ...
Acknowledgements The authors are grateful to the GenoToul Bioinformatics Platform, Toulouse, Occitanie, for providing assistance, computing and storage resources. ...
doi:10.1093/database/baz049
pmid:31032842
pmcid:PMC6487390
fatcat:xt5futbmqzb5ti24egyouuviii
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