MGE-PortalWiki/BLAST

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Informations about Sequence Databases

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Informations about Sequence Databases

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General Databases

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""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.

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""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.

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est:

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EST division of GenBank, EMBL,and DDBJ

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EST division of GenBank, EMBL,and DDBJ

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gss:

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GSS division of GenBank, EMBL,and DDBJ

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GSS division of GenBank, EMBL,and DDBJ

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htgs:

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HTG division of GenBank, EMBL,and DDBJ

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HTG division of GenBank, EMBL,and DDBJ

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env_nt Enviromental samples

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""Protein sequence databases:""

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

env_nr: Enviromental samples

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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

nt_algae est_algae: Subset of EST division of GenBank, EMBL,and DDBJ gss_algae htgs_algae

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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

nt_algae est_algae: Subset of EST division of GenBank, EMBL,and DDBJ gss_algae htgs_algae

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