MGE-PortalWiki/BLAST: Difference between revisions
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= Informations about Sequence Databases = | = Informations about Sequence Databases = | ||
== General | == General databases == | ||
==== Nucleotide sequence databases: ==== | ==== Nucleotide sequence databases: ==== | ||
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Algae specific databases contain sequences from the following taxonomic groups: | Algae specific databases contain sequences from the following taxonomic groups: | ||
a.Dinophyceae (dinoflagellates) | |||
* Chlorarachniophyceae (chlorarachniophytes), eukaryotes | * Chlorarachniophyceae (chlorarachniophytes), eukaryotes | ||
* Cryptophyta (cryptomonads), class, cryptomonads | * Cryptophyta (cryptomonads), class, cryptomonads | ||
Revision as of 20:57, 14 January 2005
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:
a.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