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Protein sequence annotation in the genome era: the annotation concept of SWISS-PROT+TREMBL

R Apweiler, A Gateau, S Contrino, M J Martin, V Junker, C O'Donovan, F Lang, N Mitaritonna, S Kappus, A Bairoch
1997 Proceedings. International Conference on Intelligent Systems for Molecular Biology  
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]

Meghana Chitale, Daisuke Kihara
2011 Protein Function Prediction for Omics Era  
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

C. H. Wu
2001 Nucleic Acids Research  
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  
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

A. Bairoch
2004 Briefings in Bioinformatics  
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

R. Apweiler
2001 Nucleic Acids Research  
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  
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

Rajesh Nair, Burkhard Rost
2004 The AI Magazine  
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

Shih-Hau Chiu, Chien-Chi Chen, Gwo-Fang Yuan, Thy-Hou Lin
2006 BMC Bioinformatics  
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  
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

Rolf Apweiler, Maria Jesus Martin, Claire O'Donovan, Manuela Pruess
2003 Pharmacogenomics (London)  
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

Alexandra M. Schnoes, Shoshana D. Brown, Igor Dodevski, Patricia C. Babbitt, Alfonso Valencia
2009 PLoS Computational Biology  
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

C P Ponting, N J Dickens
2001 Genome Biology  
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 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

Christopher Southan
2017 F1000Research  
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]

T.K. Attwood, A. Gisel, N-E. Eriksson, E. Bongcam-Rudloff
2011 Bioinformatics - Trends and Methodologies  
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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