MGE-PortalWiki/BLAST

Informations about Sequence Databases

General databases

Nucleotide sequence databases:

nt: nucleotide sequence database, with entries from all traditional divisions of GenBank, EMBL, and DDBJ excluding bulk divisions (gss, sts, pat, est, and htg divisions. wgs entries are also excluded. Not non-redundant.

est: EST division of GenBank, EMBL,and DDBJ

gss: GSS division of GenBank, EMBL,and DDBJ

htgs: HTG division of GenBank, EMBL,and DDBJ

env_nt: Enviromental samples

Protein sequence databases:

nr: non-redundant protein sequence database with entries from GenPept, Swissprot, PIR, PDF, PDB, and NCBI RefSeq

env_nr: enviromental samples

Specialized Databases

All specialized databases are subset of the general nt,est,gss,htgs, and nr databases.

Algae specific databases contain sequences from the following taxonomic groups:

• Dinophyceae (dinoflagellates)
• Chlorarachniophyceae (chlorarachniophytes), eukaryotes
• Cryptophyta (cryptomonads), class, cryptomonads
• Euglenida (euglenids), phylum, euglenoids
• Glaucocystophyceae (glaucocystophytes), class, eukaryotes
• Haptophyceae (coccolithophorids), haptophytes
• Rhodophyta (red algae), red algae
• Bacillariophyta (diatoms), phylum, diatoms
• Chrysophyceae (golden algae), class, chrysophytes
• Dictyochophyceae (silicoflagellates), class, eukaryotes
• Eustigmatophyceae (eustigmatophytes), phylum, eukaryotes
• Phaeophyceae (brown algae), phylum, brown algae
• Phaeothamniophyceae, class, eukaryotes
• Raphidophyceae (raphidophytes), class, eukaryotes
• Xanthophyceae (yellow-green algae), phylum, xanthophytes
• Chlorophyta (green algae), phylum, green algae
• Mesostigmatophyceae, class, green plants

We offer the following algae specific sequence databases:

• nt_algae: algae specific subset of GenBank, EMBL,and DDBJ (nucleotide)
• est_algae: algae specificSubset of EST division of GenBank, EMBL,and DDBJ (nucleotide)
• gss_algae: algae specific subset of GSS division of GenBank, EMBL,and DDBJ (nucleotide)
• htgs_algae :algae specific subset of HTGS division of GenBank, EMBL,and DDBJ (nucleotide)
• nr_algae: algae specific subset of NCBIs non redundant protein database

Databases of fish sequences: Fish specific databases contain sequences from the following taxonomic groups:

• Hyperotreti, chordates
• Chondrichthyes (cartilaginous fishes) class, vertebrates
• Actinopterygii (ray-finned fishes) class, bony fishes
• Hyperoartia, vertebrates

We offer the following fish sequence databases:

• nt_fishes: fishes specific subset of GenBank, EMBL,and DDBJ (nucleotide)
• est_fishes: fishes specificSubset of EST division of GenBank, EMBL,and DDBJ (nucleotide)
• gss_fishes: fishes specific subset of GSS division of GenBank, EMBL,and DDBJ (nucleotide)
• htgs_fishes :fishes specific subset of HTGS division of GenBank, EMBL,and DDBJ (nucleotide)
• nr_fishes: fishes specific subset of NCBIs non redundant protein database