NCBI BlastDB databases

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NCBI BlastDB Databases

Source: NCBI Blastdb

Name	Brief Description
nt	All Non-redundant GenBank+EMBL+DDBJ+PDB sequences (but no EST, STS, GSS, or HTGS sequences).
nr	All non-redundant GenBank CDS translations+PDB+SwissProt+PIR+PRF.
swissprot	SWISS-PROT protein sequence database.
pataa	Protein sequences derived from the Patent division of GenBank.
patnt	Nucleotide sequences derived from the Patent divison of GenBank.
pdbaa	Sequences derived from the 3-dimensional from the Protein Data Bank.
pdbnt	Sequences derived from the 3-dimensional from the Protein Data Bank.
est_human	Non-redundant Database of Human GenBank+EMBL+DDBJ EST sequences from EST Divisions.
est_mouse	Non-redundant Database of Mouse GenBank+EMBL+DDBJ EST sequences.
est_others	Non-redundant Database of all other organisms GenBank+EMBL_DDBJ EST sequences.
gss	Genome Survey Sequence, includes single-pass genomic data, exon-trapped sequences, and Alu PCR sequences.
htg	Unfinished High Throughput Genomic Sequences: phases 0, 1 and 2 (finished, phase 3 HTG sequences are in nr).
sts	Non-redundant Database of GenBank+EMBL+DDBJ STS Divisions.
month.aa	All new or revised GenBank CDS translations+PDB+SwissProt+PIR+PRF released in the last 30 days.
month.nt	All new or revised GenBank+EMBL+DDBJ+PDB sequences released in the last 30 days.
mito.aa	Database of mitochondrial sequences
mito.nt	Database of mitochondrial sequences
alu.a	Translations of select Alu repeats from REPBASE, suitable for masking Alu repeats from query sequences.
alu.n	Select Alu repeats from REPBASE, suitable for masking Alu repeats from query sequences.
drosoph.aa	Drosophila genome proteins provided by Celera and Berkeley Drosophila Genome Project (BDGP).
drosoph.nt	Drosophila genome provided by Celera and Berkeley Drosophila Genome Project (BDGP).
ecoli.aa	Escherichia coli genomic CDS translations.
ecoli.nt	Escherichia coli genomic nucleotide sequences.
vector	Vector subset of GenBank (R), NCBI, in ftp://ftp.ncbi.nlm.nih.gov/blast/db/.
yeast.aa	Yeast (Saccharomyces cerevisiae) genomic CDS translations.
yeast.nt	Yeast (Saccharomyces cerevisiae) genomic nucleotide sequences.
IgSeqProt	Kabat database of sequences of immunological interest.
IgSeqNt	Kabat database of sequences of immunological interest.
migallaaseq	Kabat database of sequences of immunological interest.
migallncseq	Kabat database of sequences of immunological interest.

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