NCBI

• National Centre for Biotechnology Information (NCBI)
  • houses a series of databases relevant to biotechnology and biomedicine and is an important resource for bioinformatics tools and services
• Entrez - Global Query Cross-Database Search System
  • molecular biology database system that provides integrated access to nucleotide and protein sequence data, gene-centred and genomic mapping information, 3D structure data, PubMed MEDLINE, and more
  • covers over 20 databases including the complete protein sequence data from PIR-International, PRF, Swiss-Prot, and PDB and nucleotide sequence data from GenBank that includes information from EMBL and DDBJ.

DNA databases

• GenBank
  • NCBI open access sequence database with an annotated collection of all publicly available nucleotide sequences and their protein translations
• European Nucleotide Archive
  • European Bioinformatics Institute (EMBL - EBI)
  • provides open data, open-source software and analytical tools, and technical infrastructure
• DNA Data Bank of Japan (DDBJ)
  • DNA database at the National Institute of Genetics in the Shizuoka prefecture of Japan

FASTA file

• text-based format for representing either nucleotide sequences or amino acide sequences

BLAST - compare DNA/protein sequences

Genome browsers

• NCBI Genome
  • information on large-scale genomics projetcs, genome sequences and assemblies, and mapped annotations, such as variations, markers and data from epigenomics studies.
• Ensembl
  • aims to provide a centralised resource for geneticists, molecular biologists and other researchers studying the genomes of our own species and other vertebrates and model organisms
  • join scientific project between the European Bioinformatics Institute and the Wellcome Trust Sanger Institute
• UCSC Genome Browser
  • includes a broad collection of vertebrate and model organism assemblies and annotations, along with a large suite of tools for viewing, analysing and downloading data.

Protein Sequence databases

• NCBI
  • protein sequence and knowledgebase
• UniProt
  • database of protein sequence and functional information, many entries being derived from genome sequencing projects
  • contains a large amount of information about the biological function of proteins derived from research literature
  • UniProt consortium comprises the European Bioinformatics Institute (EBI), the Swiss Institute of Bioinformatics (SIB) and the Protein Information Resource (PIR)
• Pfam
  • protein family database of alignments and HMMs (Sanger Institute)