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Protein sequence annotation in the genome era: the annotation concept of SWISS-PROT+TREMBL
1997
Proceedings. International Conference on Intelligent Systems for Molecular Biology
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Ongoing genome sequencing projects have dramatically increased the number of protein sequences to be incorporated into SWISS-PROT. ...
TREMBL consists of computer-annotated entries in SWISS-PROT format derived from the translation of all coding sequences (CDS) in the EMBL nucleotide sequence database, except for CDS already included in ...
The future of annotation in TREMBL Most of the sequence data nowadays is coming from genome projects and lacks biochemical evidence to provide hard data on the function of the protein. ...
pmid:9322012
fatcat:jyruj3avmrg3ljow7szl5wmjva
Computational Protein Function Prediction: Framework and Challenges
[chapter]
2011
Protein Function Prediction for Omics Era
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protein annotations. ...
We also discuss challenges in this area, first pertaining to the erroneous annotations floating in the sequence database and second regarding the limitations of the functional term vocabulary used for ...
Computational Protein Function Prediction: Framework and Challenges ...
doi:10.1007/978-94-007-0881-5_1
fatcat:scfeesrac5dnxa3desu5w6zkta
iProClass: an integrated, comprehensive and annotated protein classification database
2001
Nucleic Acids Research
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The database facilitates classification-driven annotation for protein sequence databases and complete genomes, and supports structural and functional genomic research. ...
The iProClass currently consists of more than 200 000 non-redundant PIR and SWISS-PROT proteins organized with more than 28 000 superfamilies, 2600 domains, 1300 motifs, 280 posttranslational modification ...
ACKNOWLEDGEMENTS This study is supported in part by grant DBI-9974855 from National Science Foundation, and grant P41 LM05798 from National Library of Medicine, NIH. ...
doi:10.1093/nar/29.1.52
pmid:11125047
pmcid:PMC29833
fatcat:bzntvv4tqzgafb52jdyvbp6ev4
Update on activities at the Universal Protein Resource (UniProt) in 2013
2012
Nucleic Acids Research
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discovery in the genomic and proteomic era. ...
Automatic annotation approaches UniProt has developed two complementary systems to automatically annotate the protein sequences in UniProtKB/TrEMBL. ...
Conflict of interest statement. None declared. ...
doi:10.1093/nar/gks1068
pmid:23161681
pmcid:PMC3531094
fatcat:pfzlr46jqfdlvfjtjlznfmkqsm
Swiss-Prot: Juggling between evolution and stability
2004
Briefings in Bioinformatics
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Automation: Trying to simulate the expertise of annotators Thanks to genome sequencing efforts, there has been a tremendous rise in the number of available protein sequences. ...
TrEMBL consists of computer-annotated entries derived from the translation of all Swiss-Prot contains mostly manual annotated entries TrEMBL consists of computer-annotated entries, which are not yet in ...
The NEWT Taxonomy browser Mining the server log files ...
doi:10.1093/bib/5.1.39
pmid:15153305
fatcat:3msltzin7bawlbepqj2zjzba4a
Proteome Analysis Database: online application of InterPro and CluSTr for the functional classification of proteins in whole genomes
2001
Nucleic Acids Research
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The SWISS-PROT group at EBI has developed the Proteome Analysis Database utilising existing resources and providing comparative analysis of the predicted protein coding sequences of the complete genomes ...
The two main projects used, InterPro and CluSTr, give a new perspective on families, domains and sites and cover 31-67% (InterPro statistics) of the proteins from each of the complete genomes. ...
The proteome sets are built from the SWISS-PROT and TrEMBL protein sequence databases (4) that provide reliable, well-annotated data as the basis for the analysis. ...
doi:10.1093/nar/29.1.44
pmid:11125045
pmcid:PMC29822
fatcat:ug42g6zpf5bsfoam7zavbsvlki
UniProt: the universal protein knowledgebase
2016
Nucleic Acids Research
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The UniProt knowledgebase is a large resource of protein sequences and associated detailed annotation. ...
To help interpretation of genomic variants, we provide tracks of detailed protein information for the major genome browsers. ...
UniProtKB contains more than 350 000 unique publications, with over 210 000 of these fully curated in UniProtKB/Swiss-Prot and the remainder imported in UniProtKB/TrEMBL. ...
doi:10.1093/nar/gkw1099
pmid:27899622
pmcid:PMC5210571
fatcat:hk7eqzbncray5nfbzsehqikjnm
Annotating Protein Function through Lexical Analysis
2004
The AI Magazine
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Current Opinion in Microbiology
Concept of SWISS-PROT + TREMBL. ...
The LOCKEY Algorithm.
A sequence-unique data set of localization-annotated SWISS-PROT proteins was first compiled. ...
doi:10.1609/aimag.v25i1.1746
dblp:journals/aim/NairR04
fatcat:eoinvyqphjg4zmk2jvyoiukpfa
Association algorithm to mine the rules that govern enzyme definition and to classify protein sequences
2006
BMC Bioinformatics
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The number of sequences compiled in many genome projects is growing exponentially, but most of them have not been characterized experimentally. ...
The rules may be also employed by the protein annotators in manual annotation or implemented in an automatic annotation flowchart. ...
This work is financially supported by the grant from the Ministry of Economic Affairs (Project No. 93-EC-17-A-17-R7-0563) to Food Industry Research and Development Institute. ...
doi:10.1186/1471-2105-7-304
pmid:16776838
pmcid:PMC1552092
fatcat:2v2tloebafgnzcdbksvuzk7enq
SWISS-PROT: Connecting Biomolecular Knowledge Via a Protein Database
2001
Current Issues in Molecular Biology
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In this review we will highlight our effort in connecting biological information as demonstrated in the SWISS-PROT protein database. ...
There are basically three types of sequencerelated databases (nucleic acid sequences, protein sequences and protein tertiary structures) as well as various specialized data collections. ...
Cross-References in SWISS-PROT SWISS-PROT is a curated protein sequence database, which strives to provide a high level of annotation (such as the description of the function of a protein, its domain ...
doi:10.21775/cimb.003.047
fatcat:xo4kn2lxtff75dj3qg7n6wfxtq
Managing core resources for genomics and proteomics
2003
Pharmacogenomics (London)
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In this review, we will provide examples of the core resources maintained at the EBI and summarize important issues of database management of such resources. ...
The provision of such databases as useful resources for the scientific community is a demanding task since the data not only have to be stored in a consistent way, but also have to be easily accessible ...
The most important source of information on protein sequences are the Swiss-Prot + TrEMBL protein sequence databases. ...
doi:10.1517/phgs.4.3.343.22689
pmid:12718724
fatcat:g6vudrj3hvdehj2jokjiusxkcm
Annotation Error in Public Databases: Misannotation of Molecular Function in Enzyme Superfamilies
2009
PLoS Computational Biology
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The manually curated database Swiss-Prot shows the lowest annotation error levels (close to 0% for most families); the two other protein sequence databases (GenBank NR and TrEMBL) and the protein sequences ...
Due to the rapid release of new data from genome sequencing projects, the majority of protein sequences in public databases have not been experimentally characterized; rather, sequences are annotated using ...
Meng for critical reading of the manuscript.
Author Contributions ...
doi:10.1371/journal.pcbi.1000605
pmid:20011109
pmcid:PMC2781113
fatcat:urwda7nh5zeb7ehbm7puqe54aa
Genome cartography through domain annotation
2001
Genome Biology
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To account for the great diversity of domain contexts and an unexpected paucity of ortholog conservation, we must categorize the coding regions of completely sequenced genomes into domain families, as ...
The evolutionary history of eukaryotic proteins involves rapid sequence divergence, addition and deletion of domains, and fusion and fission of genes. ...
SWISS-PROT
http://www.expasy.ch/sprot
Protein sequence databases. SWISS-PROT represents a 'gold
and Trembl
standard' of annotation. ...
pmid:11521679
fatcat:57ewcgr5obautgpysl3afg45ci
Last rolls of the yoyo: Assessing the human canonical protein count
2017
F1000Research
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However, while there have been recent cases of protein verifications from previous miss-annotation of non-coding RNA, very few have passed the Swiss-Prot curation and genome annotation thresholds. ...
The post-genomic era has seen both advances in data generation and improvements in the human reference assembly. ...
Acknowledgements The efforts of all the genomic and protein annotation teams referred to in this work are much appreciated. ...
doi:10.12688/f1000research.11119.1
pmid:28529709
pmcid:PMC5428527
fatcat:xyic6jsosze2hgbhi4aafghvkm
Concepts, Historical Milestones and the Central Place of Bioinformatics in Modern Biology: A European Perspective
[chapter]
2011
Bioinformatics - Trends and Methodologies
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Building on the ongoing sequencing work, this advance set the scene for an exciting new era in which structure determination took centre stage in our quest to understand the biophysical mechanisms that ...
In the decade that followed, time-consuming manual processes were gradually superseded with the advent of automated peptide sequencers, which increased the rate of sequence determination considerably. ...
; the UniProt Knowledgebase (UniProt), consisting of Swiss-Prot and TrEMBL, to act as the central database of protein sequences, with accurate, consistent and rich sequence and functional annotation; and ...
doi:10.5772/23535
fatcat:dwe4umftd5anrfobkciktbmg3m
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