Z-DNA research Lab

DNA links
RNA Databases:

Comparative & Phylogenetic Databases:

  • COG: Phylogenetic classification of proteins
  • DHMHD: Human-mouse homology database
  • HomoloGene: Gene homologies across species
  • Homophila: Human disease to Drosophila gene database
  • HOVERGEN: Database of homologous vertebrate genes
  • TreeBase: A database of phylogenetic knowledge
  • XREF: Cross-referencing with model organisms

SNPs, Mutations & Variations Databases:

  • ALPSbase: Database of mutations causing human ALPS
  • dbSNP: Single nucleotide polymorphism database at NCBI
  • HGVbase: Human Genome Variation database

Alternative Splicing Databases:

  • ASAP: Alternate splicing analysis tool at UCLA
  • ASG: Alternate splicing gallery
  • HASDB: Human alternative splicing database at UCLA
  • AsMamDB: alternatively spliced genes in human, mouse and rat
  • ASD: Alternative splicing database at CSHL

Specialised Databases:

  • ABIM: Links to several genomics database
  • ACUTS: Ancient conserved untranslated sequences
  • AGSD: Animal genome size database
  • AmiGO: The Gene Ontology database
  • ARGH: The acronym database
  • ASDB: Database of alternatively spliced genes
  • BACPAC: BAC and PAC genomic DNA library info
  • BBID: Biological Biochemical image database
  • Cardiac gene database:
  • CHLC: Genetic markers on chromosomes
  • COGENT: Complete genome tracking database
  • COMPEL: Composite regulatory elements in eukaryotes
  • CUTG: Codon usage database
  • dbEST: Database of expressed sequences or mRNA
  • dbGSS: Genome survey sequence database
  • dbSTS: Sequence tagged sites (STS)
  • DBTSS: Database of transcriptional start sites
  • DOGS: Database of genome sizes
  • EID: The exon-intron database - Harvard
  • Exon-Intron: Exon-Intron database - Singapore
  • EPD: Eukaryotic promotor database
  • FlyTrap: HTML based gene expression database
  • GDB: The genome database
  • GenLink: Resources for human genetic and telomere research
  • GeneKnockouts: Gene knockout information
  • GENOTK: Human cDNA database
  • GEO: Gene expression omnibus NCBI
  • GOLD: Information on genome projects around the world
  • GSDB:The Genome Sequence DataBase
  • HGI: TIGR human gene index
  • HTGS: High-through-put genomic sequence at NCBI
  • IMAGE: The largest collection of DNA sequences clones
  • IMGT: The international ImMunoGeneTics information system
  • IPCN: Index to Plant Chromosome Numbers database
  • LocusLink: Single query interface to sequence and genetic loci
  • TelDB: The telomere database
  • MitoDat: Mitochondrial nuclear genes
  • Mouse EST: NIA mouse cDNA project
  • MPSS: Searchable databases of several species
  • NDB: Nucleic acid database
  • NEDO: Human cDNA sequence database
  • NPD: Nuclear protein database
  • Oomycetes DB: Oomycetes database at Virginia Bioinformatics Institute
  • PLACE: Database of plant cis-acting regulatory DNA elements
  • RDP: Ribosomal database project
  • RDB: Receptor database at NIHS, Japan
  • Refseq: The NCBI reference sequence project
  • RHdb: Radiation hybrid physical map of chromosomes
  • SHIGAN: SHared Information of GENetic resources, Japan
  • SpliceDB: Canonical and non-canonical splice site sequences
  • STACK: Consensus human EST database
  • TAED: The adaptive evolution database
  • TIGR: Curated databases of microbes, plants and humans
  • TRANSFAC: The Transcription Factor Database
  • TRRD: Transcription Regulatory region database
  • UniGene: Cluster of sequences for unique genes at NCBI
  • UniSTS: Nonredundent collection of STS

Data bases
Major sequence data bases

  • DDBJ: DNA databank of Japan
  • EMBL: Maintained by EMBL
  • GenBank: Maintained by NCBI

protein data bases

  • Cath: Protein structure classification
  • HIV Protease: HIV protease database 3D structure
  • PDB: 3-D macromolecular structure data
  • PSI: Protein structure initiative
  • S2F: Structure to function project
  • Scop: Structural Classification of Proteins
  • BLOCKS: Multipe aligned segments of conserved protein regions
  • CCD: Conserved domain database and search service
  • DOMO: Homologous protein domain families
  • Pfam: Database of protein domains and HMMs
  • ProDom: Protein domain database
  • Prints: Protein motif fingerprint database
  • Prosite: Database of protein families and domains
  • SMART: Simple modular architecture research tool
  • TIGRFAM: Protein families based on HMMs