Categorías: Todo - databases - mutations - proteins - interactions

por MUHAMMAD HAFIZUDDIN BIN YUSOF hace 9 años

374

Nucleic Acid Research Database

The landscape of nucleic acid research databases is diverse, encompassing various types of biological data. Key resources include the NCBI Viral Genomes and VirusMentha for virus-host interactions, as well as databases focused on nucleic acid sequences like tRFdb and RNAcentral.

Nucleic Acid Research Database

Nucleic Acid Research Database

Organisational

2) Cooperation: NAR with Bioinformatics Links Directory
d) Database links are also grouped whilst arranged by scholarly citation count and social media sharing count
c) 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
b) Management improved by community efforts: suggest (new) database link; submit database; rating and review; comment and discuss; disseminate
a) Develop community-driven database public repository with contextual annotation and functional relevancy organization for establishing biologist-friendly bioinformatics ‘resourceome’
1) NAR Database Curation
e) Establishment of intuitive interconnection between the databases based on their submitted uniform-format attributes
d)Categorization of active functioning databases into eight sections to facilitate navigation as grouping the relevant databases
c) Curating conducted to update current databases’ URLs, present recent activity, merge with other databases or withdraw antiquated databases based on their responsiveness
b) Communication with owner and/or author to determine commitment on database continuation and updating
a) Semi-automated identification of dormant, non-functioning databases

Types of Database

8) others
The GOA database: Gene Ontology annotation updates for
Gene Ontology Consortium: going forward
7) Plant databases
PNRD: a plant non-coding RNA database
PLAZA 3.0: an access point for plant comparative genomics
6) Genomic variation, diseases and drugs
CancerPPD: a database of anticancer peptides and proteins
COSMIC: exploring the world's knowledge of somatic mutations in human cancer
5)Human genome, model organisms, comparative genomics
The neXtProt knowledgebase on human proteins: current status

Subtopic

DBTMEE: a database of transcriptome in mouse early embryos
4)Viruses, bacteria, protozoa, and fungi
NCBI Viral Genomes Resource
VirusMentha: a new resource for virus-host protein interactions
3) Metabolic and signalling pathways, enzymes
STRING v10: protein–protein interaction networks, integrated over the tree of life
EzCatDB: the enzyme reaction database
2) Protein sequence and structure, motifs and domains
WDSPdb: a database for WD40-repeat proteins
Expediting topology data gathering for the TOPDB database
MoonProt
1) Nucleic acid sequence, structure, and regulation
tRFdb: a database for transfer RNA fragments
RNAcentral
GenBank

Importance of Database In Describing Celullase

Genomes OnLine Database (GOLD) v.5

The provided metadatabase can serve as reference and resource for subsequent cellulase research like screening the resource(short gun sequence) for cellulase homolog families.

Novel cellulase discovery can be conducted via metagenomic approach that extracts enormous biological information from the unculturable one which is inaccessible otherwise

A four level project classification was utilized for metadata integration improvement and accommodate different sequencing projects association

Sequencing projects are catalogued and monitored whilst their metadata is stored, manually-curated and disseminated with quality control by the GOLD data management

PLAZA 3.0

Comparative genome analysis of cellulase gene families can reveal differences of phylogenetic tree among species; gene structure and location for gene homology study; transcript level for gene expression study and in general, study evolution of cellulase genes and its metabolism pathway

Various cellulase are present and expressed as participate in plant life stages like ripening and abscission. Therefore, plant genome contains rich source of novel cellulases sequence to be study

Quality (high coverage) genomic information of the 37 plant species includes gene families, protein domains, phylogenetic tree, structural and functional annotation

Comprehensive and intuitive web interface of comparative plant genomic data for facilitating data visualization, interpretation and analysis

DoRiNA 2.0—upgrading the doRiNA database of RNA interactions in post-transcriptional regulation

Due to its capacity to produce large amounts of cellulases in the biofuel production, Trichoderma reesei is increasingly being investigated for second-generation biofuel production from lignocellulosic biomass. To increase the production of cellulose, it can be done by RNA post-transcriptional regulation. By using DoRiNA 2.0, it easy to find information about RNA post-transcription regulation.

DoRiNA 2.0 is a latest version database of doRiNA database. DoRina database was upgrading to DoRina 2.0 in order to update new information of RNA interactions in post-transcriptional regulation and improve the usability of the website.

The i5k Workspace@NAL—enabling genomic data access, visualization and curation of arthropod genomes

Functional assays may involve the direct screening of gut extracts or the expression-based screening of genes identified by sequence mining.

Sequence mining is a bioinformatics approach that involves the screening of genomic, transcriptomic, or proteomic data for cellulase signatures, based on sequence and structural homology.

The 5000 arthropod genomes initiative (i5k) has tasked itself with coordinating the sequencing of 5000 insect or related arthropod genomes. The resulting influx of data, mostly from small research groups or communities with little bioinformatics experience, will require visualization, dissemination and curation, preferably from a centralized platform.

GenoBase

The GenoBase that has information of E.coli K-12 can be use to produce celulllase by making the E.coli K-12 as a host.

Designed to facilitate classification of sequenced and yet to be sequenced chromosomal regions for efficient sequencing

Which contains key information about comprehensive experimental resources of E. coli K-12, their quality control and several omics data sets generated using these resources.

The enzyme reaction database (EzCatDB)
Describing

This database includes information related to ligand molecules on the enzyme structures in the PDB data, classified in terms of cofactors, substrates, products and intermediates, which are also necessary to elucidate the catalytic mechanisms.

Application

Celullase catalyze cellulolysis, specifically; the hydrolysis of the 1,4-beta-D-glycosidic linkages in cellulose, hemicellulose, lichenin, and cereal beta-D-glucans because of that EzCatDB are useful in this proses that can identified database of hydrolysis

Reaction that can be identified this database types such as hydrolysis, transfer, addition, elimination, isomerization, hydride transfer and electron transfer have been included in the reaction classification, RLCP