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Genome Analysis: A Laboratory Manual Series Volume 1, Analyzing DNA
CHAPTER 7, Computational Analysis of DNA and Protein Sequences

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TABLE 6: Databases for Use with BLAST

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Databases	Database Sequences	Used with Program	Comments
NR	Nucleotide or protein	BLASTN BLASTP BLASTX	The non-redundant dataset contains nucleic or protein sequences from all known data sources.
MONTH	Nucleotide or protein	BLASTN BLASTP BLASTX	A 'rolling-month' dataset which represents the new records introduced to the database in the last month. Very useful for periodical verification of the databases.
SWISSPROT	Protein	BLASTP BLASTX	The Swiss-Prot protein databases.
DBEST	Nucleotide	BLASTN TBLASTN TBLASTX	The database of Expressed Sequence Tags.
DBSTS	Nucleotide	BLASTN TBLASTN TBLASTX	The database of Sequenced Tag Sites.
PDB	Protein	BLASTP BLASTX	The Brookhaven Protein database
VECTOR	Nucleotide	BLASTN	A databse of vector sequences: a useful check to do before database submissions.
KABAT	Protein	BLASTP BLASTX	Proteins of Immunological Interest.
MITO	Nucleotide	BLASTN	A database of mitochondrial DNA sequences, also a useful check to do before database submissions.
ALU	Nucleotide	BLASTN	A database of repetitive DNA sequences, also a useful check to do before database submissions. (mostly mamalian sequences)
EPD	Nucleotide	BLASTN	Eukaroytic Promoter Database

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