DATABASE Group member: Nurul Aisyah Afifah Liyana Noor Atiqah Norfariza Ronalizah
Different Type of Databases
To find out the protein domain, sequences features and 3D structures
InterPro
CATH
Database of Carbohydrate-Active enzymes which contains classification and associated information about enzymes involved in the systhesis, metabolism and transport of carbohydrates.
CAZypedia
Database of protein families that include annotation and multiple sequences aligments generated using hidden Markov models
Database resources for understanding high level function and utilities of the biological system
KEGG DRUG
KEGG DISEASES
KEGG GENES
KEGG GENOME
Database of protein sequences and functional information
UniParc
UniRef
UniProtKB
Organization of Databases in NAR
Cell Biology
CloneDB
NCBI BookShelf
Immunological Databases
MUJEN MOUSE DATABASE
Epitome
General Plant Databases
PGDD
GeneFarm
Chloroplast Genome Database
Organelle Databases
Metochondrial Genes and Protein
HMPD
MITOMAP
GOBASE
Organelle Genome
Molecular Biology Databases
Molecular Probe and Primer
VirOligo
PrimerBank
Drug and Drug Design
PharmGed
CellFinder
PubMed
Network Portal
Proteomics Resourses
MAPU
MOPED
GELBANK
Microarray Data and Other Gene Expression Databases
Sebida
HemBase
Gene Expression Barcode
Human Genes and Diseases
Cancer Gene Databases
CancerGene
MethyCancer
Protein Mutant Database
CancerResource
Human and Other Veterbrate Genomes
Human Genome Database, Maps Viewers
HOWDY
GeneAnnot
Model Organisms, Comparative Genomics
GeneSpeed
AgBase
Metabolic and Signalling Pathway
Enzyme and Enzyme nomeclature
ORENZA
BRENDA
Protein-protein Interaction
GeneNet
IBIS
ChemProt
Genomic Databases ( Non-Vertebrate)
Viral Genome Databases
ViralZone
HFV Database
The Gene Indices
MGD-mouse genomic database
Structure Databases
Protein Structure
Genome3D
DBAli
Small Molecule
DrugBank
SuperDrug
BARD
Protein Sequence Databases
Protein Properties
Cybase
REFOLD
General Sequence Databases
UniProt
RNA sequence Databases
snOPY
MeRNA
BPS
Nucleotide Sequence Databases
Transcriptional Regulator Sites and Transcription Factors
3D-Footprint
Gene Structure, introns and exon, Splice side
ECgene
GeneTack
Coding and Non-coding DNA
Patome
Dfam
International Nucleotide Sequence Database Collaboration
GenBank
BioSample
New and Updated NAR Database
Others Molecular Biology Databases
Plant Databases
Genomic Variation, Diseases and Drugs
Progenetix
NECTAR
Lynx
HbVar
FINDbase
DriverDB
canSAR
Database of Genomic Variant (DGV)
Sanger institute's DECIPHER
database of pathogenic single nucleotide variant, indels and copy-number variant
NHGRI GWAS Catalog
a curated resources of SNP-Treat Association
NCBI's ClinVar
database documenting clinically relevant sequences variant
Human Genome, Model Organisms, Comparative Genomics
Model Organism Databases
International Mouse Phenotyping Consortium (IMPC)
Vertebrate Genome Annotation (VEGA)
Mouse Phenome Database
Mouse Gene Expression Database
Mouse Genome Database (MGD)
FlyBase
WormBase
Saccharomyce Genome Database (SGD)
Human Genome
Consensus CDS Project
collaborative effort to identify a core set of human protein region
dbGaP
related to clinically relevant phenotype
database of genotyping result
Viruses, Bacteria, Protozoa and Fungi
Taxonomic
MetaRef
Sequence of Microbial Genome
BacDive
the SILVA/LTP project
Ribosomal Database Project (RDP)
Microbial Diversity in Natural Enviroment
EBI metagenomics resources
JGI'S IMG/M
Genome Annotation
Free-living Microorganism
SubtiWiki
Rhizobase
PortEco
CynoBase
Human Pathogen
SEED
PATRIC
IMG
Human Microbiome Project
Metabolics and Signalling Pathways, Enzymes, Protein Modification
Metabolics Pathway Databases
MultiTaskDB
EKPD
Merops
Carbohydrate-Active enzyme Database (CAZy)
Structure-Function Linkage Database (SFLD)
Catalytic Site Atlas
Small Molecule Pathway
Reactome
MetaCyc
Protein Sequences and Structure, Motifs and Domains, Protein-protein Interactions
protein-protein interaction
Protein SCOP Database
SCOP2
SCOP Hierarcy
SCOPe
Negatome database
NCBI (MMDB)
calculated using VAST +
protein structure database
RDBe
analysis of the electron microscopy derived structure
visualization
structural database
RNA bricks
NDB
2 new database
Repeats database
HRAP
annual update
popular database
ELM
eggNOG
uniprot and KEGG
Nucleic Acid Sequence and Structure, Transcriptional Regulation
Transcription Factor Binding Sites (TFBSs)
YEASTRACT
JASPAR
NONCODE Database
Various type of non-coding RNA
microRNA Databases
starBASE
PolymiRTS
mirTarBase
miRNEST
miRBase
Criteria that need to be fulfilled to be inserted into NAR database
Can be access without interface or paywall
must update regularly
discuss the topic of interest
Molecular biology
Structural biology
RNA
new information about the structure and biochemistry of nucleic acid binding proteins or enzymes that function in RNA metabolism
Structure,biogenesis,cellular roles and regulation of non-coding RNAs
structure assembly,mechanism of action and regulation of ribosomes,snRNPs and other stable ribonucleoprotein particles
nucleic acid enzymes
genomics
genome integrity,repair and replication
Gene regulation,chromatin and epigenetics
Computational biology
Describe the use of existing computational method to generate significant novel biological information
Description of a new algorithm that represents a substantial improvement over current methodology and has direct biological relevance
synthetic Biology and Chemistry
emerging or specialized subject areas
single molecule studies of macromolecular function
molecur machines and complex molecular assemblages
genome studies using massive parallel(Deep) sequencing
gene targeting and Genome Engineering
nuclear architecture and functional consequences
single cell gene regulation studies
Importants of Databases
Gene3D
to study the 3D structure of protein and each sequences of the structure
CAZy
determine in detailed the activity and metabolism of our protein towards carbohydrate
Pfam
can study the structure and alignment of protein
contain the family tree our protein
KEGG
study the whole function our protein
to find out the detail of biological activities of our protein
Uniprot
analyse the functional information of the protein
important to find out the sequences of our protein
