Query - Available Data Sources

The BioExtract Server gives access to data sources containing nucleotide and protein sequence data for animal and plant species. A list of the current data sources with a brief description of each is given below.

Nucleotide Sequences

• EMBL-Bank More information
  • EMBL-Bank (Last Release): The full quarterly release of all EMBL-Bank entries except MGA and EMBL-CDS entries.
  • EMBL-Bank (Update since last release): All EMBL-Bank entries created or updated after the latest EMBL-Bank release except CON, MGA or EMBL-CDS entries.
  • EMBL-Bank (Deleted Entries): Entries no longer present in the latest EMBL-Bank release.
  • EMBL-Bank (Coding Sequence): Full release of all EMBL-CDS entries.
• NCBI Nucleotide Databases More information
  • Nucleotide (nuccore): Contains all nucleotide sequences not in EST or GSS.
  • EST (Expressed Sequence Tags): Contains short single-pass reads of cDNA (transcript) sequences.
  • GSS (Genome Survey Sequences): Contains short single-pass reads of genomic DNA.
  • Nucleotide: Contains the sequence data in GenBank, EMBL and DDBJ, including all of nuccore, EST and GSS.

Protein Sequences

• NCBI Protein Database: Contains sequence data from the translated coding regions from DNA sequences in EMBL/GenBank/DDBJ, as well as protein sequences submitted to PIR, SwissProt, PRF, and PDB. More information
• UniRef: The UniProt NREF (UniProt Reference Clusters) database. In the UniRef90 and UniRef50 databases no pair of sequences in the representative set has >90% or >50% mutual sequence identity. The UniRef100 database presents identical sequences and sub-fragments as a single entry. More information
• UniProtKB: The UniProt Knowledgebase (UniProtKB) is a complete annotated protein sequence database. More information

Plant-specific nucleotides and proteins

• Miscellaneous
  • GB-PLN (DNA): GenBank plant nucleotide sequence data comprising the entire PLN division from NCBI
  • GB-PLN (protein): GenBank plant protein sequence data comprising the entire PLN division from NCBI
• Viridiplantae and Viridiplantae Protein: GB-PLN DNA and protein sequences for green plants. Data are updated monthly from NCBI.