Databases

• ***Nucleic Acids Research, January, 2025: Database Issue 
•       (see also: 2024, 2023, 2022, 2021, 
•        2020, 2019, 2018, 2017, 2016, 2015, 2014, 2013, 2012, 2011, 
•        2010, 2009, 2008, 2007, 2006, 2005, 2004, 2003, 2002, 2001)
• ***Databases listed by name or category
  
• ***Nucleic Acids Research, July, 2025: Web Server Issue
•       (see also: 2024, 2023, 2022, 2021,
  
•        2020, 2019, 2018, 2017, 2016, 2015, 2014, 2013, 2012, 2011,
•        2010, 2009, 2008, 2007, 2006, 2005, 2004, 2003)
  
• ***NCBI ***NCBI Education/Learn - NCBI News 1994-2017 - NCBI Insights 2013-
  
• ***Bioinformatics: Data's future shock - Nature, Apr 15, 2004
•       AIBG - Database and Bioinformatic Tools

Integrated Sequence Databases

• Entrez search (Maglott et al., 2005): integration of data about:
• Genes: Nucleotide sequence database (Genbank), Genomes (complete genome assemblies), PopSet (population study data sets), ProbeSet (gene expression and microarray datasets), UniSTS (markers and mapping data), SNP (single nucleotide polymorphisms);
• Proteins: Protein, (Protein sequence database), CDD (conserved domains), 3D Structure (three-dimensional macromolecular structures), 3D Domains (domains from Entrez Structure).
• Documentation: PubMed (biomedical literature) - Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders (Hamosh et al., 2005) - Online Books - Taxonomy (organisms in GenBank) - Online Mendelian Inheritance in Animals (OMIA)
• RefSeq - comprehensive, integrated, non-redundant, well-annotated set of sequences - Status Key
• Biological SOAP servers and web services provided by the public sequence data bank (Sugawara & Miyazaki, 2003)
• LocusLink - a single query interface to curated sequence and information about genetic loci.
• XREF: cross-referencing the Genetics of Model Organisms with Mammalian Phenotypes
• Expression data:  dbEST; UniGene
• TEMBLOR project at EBI (biological data integration)
• dbGaP - database of genotype and phenotype
   
• The format of Genbank flat files - Sample - Feature Table - Parser Available for GenBank Flat File
• The Information Engineering Branch (IEB) - Building NCBI's software and databases - ASN.1 - NCBI Data in XML

• SRS (Sequence Retrieval System - Service Retirement)
• EnsMart - retrieving customised data sets from annotated genomes (at Ensembl) (Kasprzyk et al., 2004)
• ARB - a software environment for sequence data (Ludwig et al., 2004)
• DNA variation: Bi-allelic sequence data | SNP - Home Page

DNA/RNA Sequences

There are three major, comprehensive database of DNA and RNA sequences; data are automatically and continuosly exchanged among them:
• European Molecular Biology Laboratories (EMBL) Nucleotide Sequence Database (Kulikova et al., 2004; Kanz et al., 2005),
now at European Bioinformatics Institute (EBI), near Cambridge, UK (Brooksbank et al., 2005; Bochrane et al., 2006);
• ***Genbank at National Center for Biotechnology Information (NCBI), Bethesda, USA (Benson et al., 2004, 2005 and 2006);
• DNA data bank of Japan (DDBJ) (click here for search), Shizuoka, Japan (Miyazaki et al., 2004; Tateno et al., 2005; Okubo et al., 2006)


• Some specialized databases for small sequences include:
• CUTG (Codon Usage Tabulated from Genbank) at Japan University
• Mitomap - mitochondrial DNA (mtDNA)
• rRNA at Gent University, Belgium (Wuyts et al., 2004)   |    rRNA at ARB
• 5S rRNA database at Pozan, Poland
  
• The Ribosomal Database Project (RDP-II) - sequences and tools for high-throughput rRNA analysis (Cole et al., 2005)
• GtRDB: The Genomic tRNA Database   |   tRNAscan-SE at Eddy Lab
• tRNA sequences and sequences of tRNA genes - August 2003 (Sprinzl and Vassilenko, 2005)
• dbSTS - A public database of Sequence Tagged Sites (short genomic landmarks)
• Official REBASE Homepage - Restriction enzyme data and recognition sites (Roberts et al., 2005)

NEBcutter - a program to cleave DNA with restriction enzymes (Vincze et al., 2003)
• UTR: Resources for analyis of 5'-UTR and 3'-UTR of eukaryotic mRNAs (Mignone et al., 2005)
• Transterm - RNA sequences and associated motifs (Jacob et al., 2006)
• SEGE - Single Exonic Genes in Eukaryotes
• Repbase (Repeated Sequences) at Genetic&"10;Information Research Institute
• L1Base - from functional annotation to prediction of active LINE-1 elements (Penzkofe et al., 2005)
• V Base - human germline variable region sequences
• The ImMunoGeneTics database (IMGT/GENE-DB) (Baum et al., 2004, Giudicelli et al., 2005, Lefranc et al., 2005)
• VBASE2 - an integrative V gene database (Retter et al., 2005)
• IPD--the Immuno Polymorphism Database (Robinson et al., 2005)
• NPRD: Nucleosome Positioning Region Database (Victor et al., 2005), at SRS

Genes Information

• HGNC - Human Genes Nomenclature Home Page
• TIGR Human Gene Index
• GeneCards: encyclopedia of genes, proteins and diseases at Weissmann Institute
• Allgenes.org - integrated database of every known and predicted human  and mouse gene
• Pseudogene.org - Comprehensive database of identified pseudogenes,
  
• Hoppsigen: a database of human and mouse processed pseudogenes (Adel et al., 2005)

MUTATIONS - DISEASES
• Human Gene Mutation Database (HGMD) at Cardiff
• Locus Specific Mutation Databases
• COSMIC - Catalogue Of Somatic Mutations In Cancer - Sanger Institute
  
• MutDB - automated SNP analysis, functionally important mutations DB, tools (Mooney and Altman, 2003)
• The TP53 Web Site - Other databases: p53 at IARC/France
• Database of Gene Knockout at Frontiers in Bioscience
• DG-CST (Disease Gene Conserved Sequence Tags) - human-mouse conserved elemenus associated to disease genes (Boccia et al., 2005)
• T1DBase - a community web-based resource for type 1 diabetes research (Smink et al., 2005)
• NCRI Informatics Initiative at National Cencer Research institute (UK)
• ROCK - Online Breast Cancer Knowledgebase
  

ONTOLOGY

What is an Ontology? - Ontology Working Group
• Gene Ontology Consortium   (2004 :update on NAR; 2006 update)

GO Annotation  (GOA) at EBI  (Camon et al., 2004)
GoFigure - query your DNA or protein sequence against the GO annotated sequences
The Cancer Genome Anatomy Project GeneOntology Browser
• Human Gene Ontology Assignments  at TIGR
• GeneMerge - functional data for a given set of genes, scores for over-representation of particular functions
• GOblet - Auuomated Gene Ontology annotation for anonymous sequence data (Hennig et al., 2003)
• Onto-Tools - Onto-Express, Onto-Compare, Onto-Design and Onto-Translate (Draghici et al., 2003)
• OntoBlast function - from sequence similarities to potential functional annotations (Zehetner, 2003)
• GOAL (Gene Ontology Automated Lexicon) - functional analysis of cDNA microarrays - University of Ferrara
• PA-GOSUB - model :organism protein sequences with their predicted Gene Ontology (Lu et al., 2005)
• ChipInfo- organizing information from online databases into easily interpretable tabular format outputs 

Genes Expression data

• NCBI Gene Expression Omnibus (GEO) - Archive for gene expression and epigenomics data sets
• NCBI GEO (Edgar et al., 2002; Barrett and Edgar, 2006; Clough and Barrett 2016; Clough et al., 2024)
• The Expressed Gene Anatomy Database (EGAD)
• dbEST - "Single-pass" cDNA sequences or Expressed Sequence Tags at NCBI
• Mouse Genome Informatics - Gene Expression Data

Vectors

• VECTORS database

Eucaryotic Promoters

• TRANSFAC - The Transcription Factor Database (Matys et al., 2006)
• WWW Promoter Scan
• The Eucaryotic Promoter Database (EPD) (search; search by SRS under "Nucleotide related databases") (Schmid et al., 2004, 2006)
• WWW SIGNAL SCAN Databases - Web Signal Scan Service)
• Promoter Analysis and Recognition at Genomatix.de
• Effects of promoter sequence elements on mRNA transcription (Lapidot & Pilpel, 2003)
• PromH - promoters identification using orthologous genomic sequences (Solovyev & Shahmuradov, 2003)
• SiteSeer - visualisation and analysis of transcription factor binding sites in nucleotide sequences (Boardman et al., 2003)
• MATCHTM - a tool for searching transcription factor binding sites in DNA sequences (Kel et al., 2003)
• Gibbs Recursive Sampler - finding transcription factor binding sites (Thompson et al., 2003)
• YMF - discovery of novel transcription factor binding sites by statistical overrepresentation (Sinha & Tompa, 2003)
• Target Explorer - identification of new target genes for a specified set of transcription factors (Sosinsky et al., 2003)
• RSAT - Regulatory Sequence Analysis Tools (van Helden, 2003)
• TRED - a Transcriptional Regulatory Element Database for in silico studies (Zhao et al., 2005)
• The MAPPER database - a multi-genome catalog of putative transcription factor binding sites (Marinescu et al., 2005)
• Dragon ERE Finder version 2 - detection and analysis of estrogen response elements in vertebrate genomes (Bajic et al., 2003)

 
• FIE2 - extraction of genomic DNA sequences around the start and translation initiation site of human genes (Chong et al., 2003)
• PromoSer - a large-scale mammalian promoter and transcription start site identification service (Halees et al., 2003)
• Dragon Gene Start Finder - approximate locations of the 5' ends of genes (Bajic & Seah, 2003)
• DoOP - Databases of Orthologous Promoters - upstream sequences (Barta et al., 2005)

 
•  JASPAR: an open-access database for eukaryotic transcription factor binding profiles (Sandelin et al., 2004)
•  TrSDB: a proteome database of transcription factors (Hermoso wt al., 2004)

RNA/DNA Structure

• Biological Structure Resource
• WEB-THERMODYN - sequence analysis for profiling DNA helical stability (Huang & Kowalski, 2003)
• Image library of biological macromolecules (RNA) at Jena University, Germany.
• The RNA World Website
• RNA secondary structure - at Sequence Analysis with Distributed Resources
• Thermodynamics, software and databases for RNA structure
• RNA-related tools on the Bielefeld Bioinformatics Server (Sczyrba et al., 2003)

 
• RNA and DNA folding and hybridization prediction server mfold by M. Zuker (Zuker, 2003) - RNAfold at Vienna
• RNAsoft - a suite of RNA secondary structure prediction and design software tools (Andronescu et al., 2003)
• Pfold - RNA secondary structure prediction using stochastic context-free grammars (Knudsen & Hein, 2003)
• Structurelab - RNA structure analysis and comparison (including Stem Trace) -
• Vienna RNA secondary structure server - Vienna RNA Package (Hofacker, 2003)
• PSEUDOVIEWER2 - visualization of RNA pseudoknots of any type (Han & Byun, 2003)
• GPRM - a genetic programming approach to finding common RNA secondary structure elements (Hu, 2003)
• Tools for the automatic identification and classification of RNA base pairs (Yang et al., 2003)
• A software tool-box for analysis of regulatory RNA elements (Bengert & Dandekar, 2003)
• RNA Secondary Structure as a Reusable Interface to Biological Information Resources - Felciano, Chen & Altman
• SVMPredict - An antisense oligonucleotide prediction tool using Support Vector Machines (Camps-Valls, 2004)

Software
• RNAdraw

PROTEIN Sequences

• UniProt (Universal Protein Resource) - (Apweiler et al., 2004; Bairoch et al., 2005)
• Protein Information Resource Home Page at NBRF (National Biomedical Research Foundation, USA)
• PRF Protein Research Foundation (Osaka, Japan).
• OWL (non-redundant protein sequences database) at University of Manchester, UK

PROTEIN Structures

• Protein Data Bank (3D structures of proteins)
• Human Protein Reference Database (HPRD) (Mishra et al., 2006)
• The RCSB Protein Data Bank - query system and relational database (mmCIF schema) (Deshpande et al., 2005)
• PDBsum more - new summaries and analyses of the known 3D structures of proteins and nucleic acids (Laskowski et al., 2005)
• PDB-Ligand - a ligand database based on PDB for classification of ligand-binding structures (Shin and Cho, 2005)
• E-MSD (EBI Macromolecular Structure Database - an integrated data resource for bioinformatics  (Velankar et al., 2005)
• STING Report - graphic and tabular presentations of protein sequence, structure and function (Neshich et al., 2005)
• SWISS-3DIMAGE at Geneva University Switzerland - Database of annotated 3D protein images
• Protein Structure Analysis at Department of Biochemistry and Molecular Biology University College London
• SCOP search and retrieval at Cambridge UK Structural Classification of Proteins
• NRL-3D - sequence and 3D structures of proteins by PIR
• SWISS-MODEL - Molecular Modeling on-line
• STRUCTURE at NCBI

PROTEOME Expression


• Human Proteome Map (HPM) (Kim et al., 2014)
• Human Body Map in Proteomics DB (Wilhelm et al., 2014)
  

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Last updated January 6, 2023 (work in progress)

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