What is TrEMBL?
Introduction TrEMBL is a computer-annotated protein sequence database supplementing the SWISS-PROT Protein Sequence Data Bank. TrEMBL contains the translations of all coding sequences (CDS) present in the EMBL Nucleotide Sequence Database not yet integrated in SWISS-PROT.
What is the difference between SWISS-PROT and TrEMBL?
TrEMBL consists of entries in a SWISS-PROT format that are derived from the translation of all coding sequences in the EMBL nucleotide sequence database, that are not in SWISS-PROT. Unlike SWISS-PROT entries those in TrEMBL are awaiting manual annotation.
Is TrEMBL a primary database?
TrEMBL database (primary databases)
Is TrEMBL a nucleotide sequence database?
TrEMBL consists of computer-annotated entries in SWISS-PROT-like format derived from the translation of all coding sequences (CDS) in the EMBL nucleotide sequence database, except for CDS already included in SWISS-PROT.
How many sequences are in TrEMBL?
TrEMBL contains 755 169 sequence entries (SP-TrEMBL: 685 601; REM-TrEMBL: 79 568), TrEMBLnew contains 93 546 entries.
Is TrEMBL a reviewed database?
UniProtKB/TrEMBL (unreviewed) contains protein sequences associated with computationally generated annotation and large-scale functional characterization.
How do I access TrEMBL?
Access the UniProtKB/TrEMBL DatabaseSRS - is the easiest and simplest method available to quickly access the UniProtKB/TrEMBL sequence database.UniProt Power Search - Provides full text, advanced search, set manipulation and search filtering on the Universal Protein Resource.
What is PDB used for?
The PDB distributes coordinate data, structure factor files and NMR constraint files. In addition it provides documentation and derived data. The coordinate data are distributed in PDB and mmCIF formats.
What is PDB in bioinformatics?
Protein Data Bank (PDB) is the single worldwide archive of structural data of biological macromolecules. It includes data obtained by X-ray crystallography and nuclear magnetic resonance (NMR) spectrometry submitted by biologists and biochemists from all over the world.
What is EMBL and GenBank?
The European Molecular Biology Laboratory (EMBL) Nucleotide Sequence Database (http://www.ebi.ac. uk/embl/index. html ) is maintained at the European Bioinformatics Institute (EBI) in an international collaboration with the DNA Data Bank of Japan (DDBJ) and GenBank (USA).
What is UniProt in bioinformatics?
The Universal Protein Resource (UniProt) is a comprehensive resource for protein sequence and annotation data. The UniProt databases are the UniProt Knowledgebase (UniProtKB), the UniProt Reference Clusters (UniRef), and the UniProt Archive (UniParc).
What is a bioinformatic?
Bioinformatics is defined as the application of tools of computation and analysis to the capture and interpretation of biological data. It is an interdisciplinary field, which harnesses computer science, mathematics, physics, and biology (fig 1).
Is UniProt a secondary database?
Hybrid databases and families of databases Many data resources have both primary and secondary characteristics. For example, UniProt accepts primary sequences derived from peptide sequencing experiments.
What is SWISS-PROT protein sequence database?
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 domains structure, post-translational modifications, variants, etc.), a minimal level of redundancy and high level of integration with other databases.
What is UniGene in bioinformatics?
UniGene is an experimental system for automatically partitioning GenBank sequences into a non-redundant set of gene-oriented clusters. Each UniGene cluster contains sequences that represent a unique gene, as well as related information such as the tissue types in which the gene has been expressed and map location.
What type of data is accessible through SCOP?
The SCOP database is freely accessible on the internet. SCOP was created in 1994 in the Centre for Protein Engineering and the Laboratory of Molecular Biology....Structural Classification of Proteins database.ContentWebsitehttps://scop.berkeley.eduMiscellaneousVersion2.07 (March 2018; 276,231 domains in 87,224 structures classed as 4,919 families)6 more rows
What are the tools used to manipulate biological data?
Several computer tools are there to manipulate the biological data like an update, delete, insert, etc. Scientists, researchers from all over the world enter their experiment data and results in a biological database so that it is available to a wider audience.
Why is a biological database useful?
Uses of biological Databases : It helps the researchers to study the available data and form a new thesis, anti-virus, helpful bacteria, medicines, etc. It helps scientists to understand the concepts of biological phenomena. The database acts as a storage of information. It helps remove the redundancy of data.
Abstract
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 structure, post-translational modifications, variants, etc), a minimal level of redundancy and a high level of integration with other databases.
Introduction
SWISS-PROT ( 1 ) is an annotated protein sequence database established in 1986 and maintained collaboratively, since 1987, by the Department of Medical Biochemistry of the University of Geneva and the EMBL Data Library (now the EMBL Outstation-The European Bioinformatics Institute; 2 ).
Recent Developments
We have selected a number of organisms that are the target of genome sequencing and/or mapping projects and for which we intend to: (i) be as complete as possible (all sequences available at a given time should be immediately included in SWISS-PROT, including sequence corrections and updates); (ii) provide a higher level of annotation; (iii) cross-reference to specialized databases that contain, among other data, some genetic information about the genes that code for these proteins; (iv) provide specific indices or documents..
Practical Information
Release 32.0 of SWISS-PROT (October 1995) contains 48 440 sequence entries, comprising 17 000 000 amino acids abstracted from ∼43 000 references. The data file (sequences and annotations) requires 90 Mb disk storage space. The documentation and index files require ∼30 Mb disk space. No restrictions are placed on use or redistribution of the data.
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What is a trEMBL?
UniProtKB/TrEMBL contains high-quality computationally analyzed records, which are enriched with automatic annotation. It was introduced in response to increased dataflow resulting from genome projects, as the time- and labour-consuming manual annotation process of UniProtKB/Swiss-Prot could not be broadened to include all available protein sequences. The translations of annotated coding sequences in the EMBL-Bank/GenBank/DDBJ nucleotide sequence database are automatically processed and entered in UniProtKB/TrEMBL. UniProtKB/TrEMBL also contains sequences from PDB, and from gene prediction, including Ensembl, RefSeq and CCDS.
What is UniProt database?
UniProt is a freely accessible database of protein sequence and functional information, many entries being derived from genome sequencing projects. It contains a large amount of information about the biological function of proteins derived from the research literature.