Nucleic Acid Research Database

The enzyme reaction database (EzCatDB)

Describing

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

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

Describing

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.

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

Application

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.

Describing

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.

Application

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.

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

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

Describing

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.

Application

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.

PLAZA 3.0

Describing

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

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

Application

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

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

Describing

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

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

Application

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

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

GenBank

RNAcentral

tRFdb: a database for transfer RNA fragments

2) Protein sequence and structure, motifs and domains

MoonProt

Expediting topology data gathering for the TOPDB database

WDSPdb: a database for WD40-repeat proteins

EzCatDB: the enzyme reaction database

STRING v10: protein–protein interaction networks, integrated over the tree of life

VirusMentha: a new resource for virus-host protein interactions

NCBI Viral Genomes Resource

5)Human genome, model organisms, comparative genomics

DBTMEE: a database of transcriptome in mouse early embryos

The neXtProt knowledgebase on human proteins: current status

6) Genomic variation, diseases and drugs

COSMIC: exploring the world's knowledge of somatic mutations in human cancer

CancerPPD: a database of anticancer peptides and proteins

PLAZA 3.0: an access point for plant comparative genomics

PNRD: a plant non-coding RNA database

8) others

Gene Ontology Consortium: going forward

The GOA database: Gene Ontology annotation updates for

1) NAR Database Curation

a) Semi-automated identification of dormant, non-functioning databases

b) Communication with owner and/or author to determine commitment on database continuation and updating

c) Curating conducted to update current databases’ URLs, present recent activity, merge with other databases or withdraw antiquated databases based on their responsiveness

d)Categorization of active functioning databases into eight sections to facilitate navigation as grouping the relevant databases

e) Establishment of intuitive interconnection between the databases based on their submitted uniform-format attributes

a) Develop community-driven database public repository with contextual annotation and functional relevancy organization for establishing biologist-friendly bioinformatics ‘resourceome’

b) Management improved by community efforts: suggest (new) database link; submit database; rating and review; comment and discuss; disseminate

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

d) Database links are also grouped whilst arranged by scholarly citation count and social media sharing count