Nucleic Acids Research Database
Type of Database
Type VIII : Other Databases
Why it is useful- This database provides:
Describe protein function including catalytic activity and etc.
Annotating protein and gene names
Determination of annotation rule
Determination of family membership of protein sequence
Description- This database provides automatic classification and annotation of protein sequences. It also allows precise annotation of individual functional variants within large homologous protein families.
Identified database- HAMAP ( High-Quality Automated and Manual Annotation of Proteins) (http://hamap.expasy.org)
Type VII : PLANT DATABASE
Pepsin are part of the cleavage process. Pepsin also cleaves nonheme iron which is found in plant foods such as cereals, fruits and vegetables from a protein to facilitate absorption.
Description
Structural and functional annotation, gene families, protein domains, phylogenetic trees and detailed information about genome organization can easily be queried and visualized.
Designed to make comparative genomics data for plants available through a user-friendly web interface.
identified database : Plaza 3.0 (http://bioinformatics.psb.ugent.be/plaza/versions/plaza_v3_dicots/a)
Type VI : Genomic variation, diseases and drugs
Identified Database: CancerPPD (http://crdd.osdd.net/raghava/cancerppd/)
Why it is useful?
3. Complex query, facilitate users who wish to perform complex search to extract the desired information from CancerPPD
2. Simple search, provides basic facility to retrieve data from the database. It allows users to perform keyword search on any field of the database
1. Has peptide sequence search, which allow researcher to searching given peptide sequence against sequences of all peptides available in CancerPPD
Type V : Human genome, model
organisms, comparative genomics.
Provide many information.
Very easy to use.
It shows various types of a protein including it’s definition, function, and process which the protein involve.
Description : it is a database that provide various types of information on human proteins.
Identified database : neXtProt (http://www.nextprot.org/)
Type IV : Viruses, Bacteria, Protozoa and Fungi
Why it is useful- This database give information about the protein ( acidin-pepsin) also known as glycine betaine
Metabolic reaction of this compound
Monoisotopic molecular weight
Molecular weight
It chemical formula
It molecular group
Description- This database describes the generic and condition-specific metabolic network of Trypanosoma brucei ( a parasitic protozoan) responsible for human and animal African Trypanosomiasis ( common known as sleeping sickness).
Identified database- TrypanoCyc (www.metexplore.fr/trypanocyc)
Type III : Metabolic and signalling pathways , enzymes.
the enzyme induces cleavage of gluten-derived peptides predigested by pepsin and pancreatic enzymes an exhibiting a detoxifying effect in the host's gut.
identified databese : BRENDA databes (http://www.brenda-enzymes.org)
Type II : Protein sequence and structure, motifs and domains.
2. Can avoid the redundancy of multiple copies of protein in same databases or different databases by storing the protein in stable and unique identifier (UPI)
1. Central hub for the collection of functional information on proteins, with accurate, consistent and rich annotation
Description : 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). The UniProt Metagenomic and Environmental
Sequences (UniMES) database is a repository specifically developed for metagenomic and environmental data.
Identified Database: UniProt (http://www.uniprot.org/)
Type I : Nucleic acid sequence, structure, and regulation
Why it is useful
By using Entrez to explore GenBank, it maintains a history of your search, and allows you to combine and modify previous searchesand look at other resources provided by NCBI. Entrez is an important integrated database provided by NCBI, and provides powerful tools to find and explore biotechnology information.
Minimal delay in accessing latest information.
Publicly available, can be used freely by anyone.
Provide nucleotide sequences and their protein translations in various organisms.
Description : Database that contains nucleotide sequences obtained through submissions from individual laboratories and batch submissions from large scale sequencing projects.
Identified database : GenBank (http://www.ncbi.nlm.nih.gov/genbank/)
Organization
Cooperation: NAR with Bioinformatics Links Directory
Database links are also grouped whilst arranged by scholarly citation count and social media sharing count
Cataloguing databases on their functions and features by categorizing into relevant, representative biological subject; retrieving search result via matching queried phrase to similar word in link’s title, description or tags
Management improved by community efforts: suggest (new) database link; submit database; rating and review; comment and discuss; disseminate
Develop community-driven database public repository with contextual annotation and functional relevancy organization for establishing biologist-friendly bioinformatics ‘resourceome’
NAR Database Curation
Establishment of intuitive interconnection between the databases based on their submitted uniform-format attributes
Categorization of active functioning databases into eight sections to facilitate navigation as grouping the relevant databases
Curating conducted to update current databases’ URLs, present recent activity, merge with other databases or withdraw antiquated databases based on their responsiveness
Communication with owner and/or author to determine commitment on database continuation and updating
Semi-automated identification of dormant, non-functioning databases
