{"id":73,"date":"2025-01-11T09:25:46","date_gmt":"2025-01-11T09:25:46","guid":{"rendered":"https:\/\/pokharelsugam.com.np\/bioinformatics\/?p=73"},"modified":"2025-12-16T10:46:24","modified_gmt":"2025-12-16T05:01:24","slug":"bioinformatics-databases-types","status":"publish","type":"post","link":"https:\/\/pokharelsugam.com.np\/bioinformatics\/bioinformatics-databases-types\/","title":{"rendered":"Types and Lists of Bioinformatics  Databases"},"content":{"rendered":"\n<h2 class=\"wp-block-heading\">Bioinformatics Databases<\/h2>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Human Genomic Browser<\/strong><\/p>\n\n\n\n<p class=\"wp-block-paragraph\">NCBI : <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/gdv\/\">https:\/\/www.ncbi.nlm.nih.gov\/gdv\/<\/a><\/p>\n\n\n\n<p class=\"wp-block-paragraph\">UCSC: <a href=\"https:\/\/genome-asia.ucsc.edu\/\">https:\/\/genome-asia.ucsc.edu\/<\/a><\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Sequence Database (Nucleotide or Amino Acid Sequence)<\/strong> : Main Domain <\/p>\n\n\n\n<p class=\"wp-block-paragraph\">GenBank&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/\">https:\/\/www.ncbi.nlm.nih.gov\/<\/a> (All Databases, Primary Database)<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">Ensembl&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <a href=\"https:\/\/www.ensembl.org\/\">https:\/\/www.ensembl.org\/<\/a> (Nucleotide sequences)<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">DDBJ                    <a href=\"https:\/\/www.ddbj.nig.ac.jp\/\">https:\/\/www.ddbj.nig.ac.jp\/<\/a> (Nucleotide sequences, Primary Database)<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">EMBL-EBI&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <a href=\"https:\/\/www.ebi.ac.uk\/\">https:\/\/www.ebi.ac.uk\/<\/a> (Nucleotide sequences, Primary Database)<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">UniProt&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <a href=\"https:\/\/www.uniprot.org\/\">https:\/\/www.uniprot.org\/<\/a> (Amino Acid Sequence, Secondary Database)<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">BV-BRC    <a href=\"https:\/\/www.bv-brc.org\/\">https:\/\/www.bv-brc.org\/<\/a> (Bacterial and Viral Bioinformatics Resource)<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">BacDive     <a href=\"https:\/\/bacdive.dsmz.de\/\">https:\/\/bacdive.dsmz.de\/<\/a> (Bacterial Diversity Metadata)<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Sequence Database (Nucleotide or Amino Acid Sequence)<\/strong>: Sub Domain<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">ENA     <a href=\"https:\/\/www.ebi.ac.uk\/ena\/browser\/home\">https:\/\/www.ebi.ac.uk\/ena\/browser\/home<\/a> (Genomes, Transcriptomes)<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">Ensembl Bacteria       <a href=\"https:\/\/bacteria.ensembl.org\/index.html\">https:\/\/bacteria.ensembl.org\/index.html<\/a>       (Gene and Genome of Bacteria)<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">NCBI-RefSeq     <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/refseq\/\">https:\/\/www.ncbi.nlm.nih.gov\/refseq\/<\/a> (Genome. Transcriptome)<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">NCBI-GEO DataSets     <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/gds\/\">https:\/\/www.ncbi.nlm.nih.gov\/gds\/<\/a> (Curated gene expression DataSets)<\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Structural Database (Protein Structure)<\/strong><\/p>\n\n\n\n<p class=\"wp-block-paragraph\">Protein Data Bank (PDB)&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <a href=\"https:\/\/www.rcsb.org\/\">https:\/\/www.rcsb.org\/<\/a>&nbsp; (3D structure, Primary Database)<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">SCOP&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <a href=\"http:\/\/scop.mrc-lmb.cam.ac.uk\/scop\/\">http:\/\/scop.mrc-lmb.cam.ac.uk\/scop\/<\/a> (Structural classifications)<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">CATH&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <a href=\"https:\/\/www.cathdb.info\/\">https:\/\/www.cathdb.info\/<\/a>&nbsp; (Hierarchical classification)<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">AlphaFold     <a href=\"https:\/\/alphafold.ebi.ac.uk\/\">https:\/\/alphafold.ebi.ac.uk\/<\/a><\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Functional Annotation (Gene\/Protein Annotation)<\/strong><\/p>\n\n\n\n<p class=\"wp-block-paragraph\">Gene Ontology (GO)&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <a href=\"http:\/\/geneontology.org\/\">http:\/\/geneontology.org\/<\/a><\/p>\n\n\n\n<p class=\"wp-block-paragraph\">InterPro&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <a href=\"https:\/\/www.ebi.ac.uk\/interpro\/\">https:\/\/www.ebi.ac.uk\/interpro\/<\/a><\/p>\n\n\n\n<p class=\"wp-block-paragraph\">KEGG&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <a href=\"https:\/\/www.genome.jp\/kegg\/\">https:\/\/www.genome.jp\/kegg\/<\/a><\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Genomic and Variation (Genetic Variation)<\/strong><\/p>\n\n\n\n<p class=\"wp-block-paragraph\">dbSNP&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/snp\/\">https:\/\/www.ncbi.nlm.nih.gov\/snp\/<\/a><\/p>\n\n\n\n<p class=\"wp-block-paragraph\">1000 Genomes Project&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <a href=\"https:\/\/www.internationalgenome.org\/\">https:\/\/www.internationalgenome.org\/<\/a><\/p>\n\n\n\n<p class=\"wp-block-paragraph\">ClinVar&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/clinvar\/\">https:\/\/www.ncbi.nlm.nih.gov\/clinvar\/<\/a><\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Expression Database (Gene Expression)<\/strong><\/p>\n\n\n\n<p class=\"wp-block-paragraph\">Gene Expression Omnibus (GEO)&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/geo\/\">https:\/\/www.ncbi.nlm.nih.gov\/geo\/<\/a><\/p>\n\n\n\n<p class=\"wp-block-paragraph\">ArrayExpress&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <a href=\"https:\/\/www.ebi.ac.uk\/arrayexpress\/\">https:\/\/www.ebi.ac.uk\/arrayexpress\/<\/a><\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>&nbsp;Phylogenetic Database<\/strong><\/p>\n\n\n\n<p class=\"wp-block-paragraph\">iTOL     <a href=\"https:\/\/itol.embl.de\/itol.cgi\">https:\/\/itol.embl.de\/itol.cgi<\/a><\/p>\n\n\n\n<p class=\"wp-block-paragraph\">TreeBASE&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <a href=\"https:\/\/treebase.org\/\">https:\/\/treebase.org\/<\/a><\/p>\n\n\n\n<p class=\"wp-block-paragraph\">Silva&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <a href=\"https:\/\/www.arb-silva.de\/\">https:\/\/www.arb-silva.de\/<\/a><\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Metabolic and Pathway<\/strong><\/p>\n\n\n\n<p class=\"wp-block-paragraph\">Reactome&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <a href=\"https:\/\/reactome.org\/\">https:\/\/reactome.org\/<\/a><\/p>\n\n\n\n<p class=\"wp-block-paragraph\">BioCyc&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <a href=\"https:\/\/biocyc.org\/\">https:\/\/biocyc.org\/<\/a><\/p>\n\n\n\n<p class=\"wp-block-paragraph\">Drug Discovery<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">DrugBank&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <a href=\"https:\/\/www.drugbank.ca\/\">https:\/\/www.drugbank.ca\/<\/a><\/p>\n\n\n\n<p class=\"wp-block-paragraph\">ChEMBL&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <a href=\"https:\/\/www.ebi.ac.uk\/chembl\/\">https:\/\/www.ebi.ac.uk\/chembl\/<\/a><\/p>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Species Specific<\/strong><\/p>\n\n\n\n<p class=\"wp-block-paragraph\">FlyBase &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <a href=\"https:\/\/flybase.org\/\">https:\/\/flybase.org\/<\/a>&nbsp;&nbsp; (Drosophila species)<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">WormBase&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <a href=\"https:\/\/wormbase.org\/\">https:\/\/wormbase.org\/<\/a>&nbsp; (<em>Caenorhabditis elegans<\/em> species)<\/p>\n\n\n\n<p class=\"wp-block-paragraph\">TAIR&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <a href=\"https:\/\/www.arabidopsis.org\/\">https:\/\/www.arabidopsis.org\/<\/a>&nbsp; (Arabidopsis thaliana)<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">Chemoinformatics Databases<\/h2>\n\n\n\n<p class=\"wp-block-paragraph\">DrugBank    <a href=\"https:\/\/go.drugbank.com\/\">https:\/\/go.drugbank.com\/<\/a><\/p>\n\n\n\n<p class=\"wp-block-paragraph\">PubChem    <a href=\"https:\/\/pubchem.ncbi.nlm.nih.gov\/\">https:\/\/pubchem.ncbi.nlm.nih.gov\/<\/a><\/p>\n\n\n\n<p class=\"wp-block-paragraph\">ChEMBL    <a href=\"https:\/\/www.ebi.ac.uk\/chembl\/\">https:\/\/www.ebi.ac.uk\/chembl\/<\/a><\/p>\n\n\n\n<p class=\"wp-block-paragraph\">ZINC Database:    <a href=\"  https:\/\/zinc.docking.org\/substances\/\">https:\/\/zinc.docking.org\/substances\/<\/a><\/p>\n\n\n\n<p class=\"wp-block-paragraph\">ChemSpider    <a href=\"https:\/\/www.chemspider.com\/\">https:\/\/www.chemspider.com\/<\/a><\/p>\n\n\n\n<p class=\"wp-block-paragraph\">BindingDB     <a href=\"https:\/\/www.bindingdb.org\/rwd\/bind\/BindingDBRESTfulAPI.jsp\">https:\/\/www.bindingdb.org\/rwd\/bind\/BindingDBRESTfulAPI.jsp<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"<p>Bioinformatics Databases Human Genomic Browser NCBI : https:\/\/www.ncbi.nlm.nih.gov\/gdv\/ UCSC: https:\/\/genome-asia.ucsc.edu\/ Sequence Database (Nucleotide or Amino Acid Sequence) : Main Domain [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_uag_custom_page_level_css":"","site-sidebar-layout":"default","site-content-layout":null,"ast-site-content-layout":"default","site-content-style":"default","site-sidebar-style":"default","ast-global-header-display":"","ast-banner-title-visibility":"","ast-main-header-display":"","ast-hfb-above-header-display":null,"ast-hfb-below-header-display":"","ast-hfb-mobile-header-display":"","site-post-title":"","ast-breadcrumbs-content":null,"ast-featured-img":"","footer-sml-layout":"","ast-disable-related-posts":"","theme-transparent-header-meta":"","adv-header-id-meta":null,"stick-header-meta":null,"header-above-stick-meta":null,"header-main-stick-meta":null,"header-below-stick-meta":null,"astra-migrate-meta-layouts":"default","ast-page-background-enabled":"default","ast-page-background-meta":{"desktop":{"background-color":"var(--ast-global-color-5)","background-image":"","background-repeat":"repeat","background-position":"center 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