Databases available for BLAST searching at UTHSCSA

Peptide Sequence Databases

Described by NCBI as "All non-redundant GenBank CDS translations+PDB+SwissProt+PIR+PRF"  Protein nr contains essentially all the protein entries that there are.  The same sequence may be present with different gi numbers as a GenBank entry, an EMBL entry, a SwissProt entry, etc.  The "nonredundant" aspect of the organization is that the actual sequence for redundant entries is only represented once, hence only searched once.  If matched in a blast search, links to all the entries corresponding to that sequence are then given.

Same as nr, but one entry per sequence even if the sequence is identical to another entry.  It is not obvious that there would be any reason to burn the extra search time to search this library.  Its main utility may be for use with fastacmd to retrieve sequences with clean definition lines.

A single curated set (NCBI's RefSeq set) of Yeast (Saccharomyces cerevisiae) protein sequences.  Compared to searching nr with "Saccharomyces cerevisiae"[orgn] in the Entrez query field, searching yeast.aa is faster, but will only show links to RefSeq entries.  The latter may find additional yeast protein sequences that RefSeq curators chose not to include.

A single curated set (NCBI's RefSeq set) of E.coli K12 genes.  See yeast.aa for implications relative to limiting by Entrez query.

A single curated set (NCBI's RefSeq set) of Drosophila melanogaster genes. See yeast.aa for implications relative to limiting Entrez query.

Mitochondrially encoded proteins.

Translations of select Alu repeats from REPBASE, suitable for masking Alu repeats from query sequences. It is available by anonymous FTP from ncbi.nlm.nih.gov (under the /pub/jmc/alu directory). See "Alu alert" by Claverie and Makalowski, Nature vol. 371, page 752 (1994) .

Sequences submitted in support of patent applications.

Same as env_nr, but one sequence per definition line.

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Nucleotide Sequence Databases

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nr

No longer supported.  nr for nucleotides was a union of essentially every division below.  One can construct a search of any arbitrary union of divisions using command line blast.

nt

nt contains all the spliced sequences inferred from genomic sequences.

human_genomic

23 entries representing the RefSeq version of the human chromosomes.  Gaps of undefined size are represented by strings of 100 N's.

other_genomic

Complete chromosomes or genomes from many bacteria, viruses, bacteriophages, plasmids, yeast, drosophila, Arabidopsis, and C. elegans.  Notably missing are mammals or Zebrafish. See this link for a 11/30/2004  listing of the genomes and chromosomes in "other_genomic".  For partially finished genomes, fragmentary sequences can be found in htgs and wgs divisions below.  However, there may be more organized "freezes" or "builds" curated to remove redundancies and group sequences by their respective chromosomes.  Check NCBI genome resources to see if such a dataset exists and if a special Blast page exists for searching it there.  On request, we can import such datasets for local access.

yeast.nt
The RefSeq entries for the Saccharomyces cerevisiae chromosomes.
ecoli.nt
The RefSeq entry for the E. coli chromosome.
drosoph.nt

The RefSeq enties for the Drosophila melanogaster chromosomes.

est

The union of the 3 est division below.

est_human

Expressed sequence tags from humans.  There may be many entries for each gene, but in contrast to nt, only sequences corresponding to cDNA clones that actually exist are included.

est_mouse
est_others
pdbnt

Nucleotide sequences corresponding to protein sequences in the Brookhaven Protein Databank.

igSeqNt

Nucleotide sequences from Kabat's database of sequences of immunological interest

vector

Sequences of plasmids, etc. used as cloning vectors.

sts

A separate collection of short genomic sequences entered with primer information as Sequence Tagged Sites.

gss

Genome Survey Sequences, includes single-pass genomic data, exon-trapped sequences, and Alu PCR sequences.

htgs

A collection of partially assembled sequences from the genome centers.  These sequences are organized by Bac, or other large insert clone.  See notes under "other_genomic" for alternatives to searching htgs.

wgs

Another collection of partially assembled sequences from the genome centers.  These are contigs assembled directly from whole genome shotgun sequencing.  See notes under "other_genomic" for alternatives to searching wgs.

mito.nt
mitochondrial sequences
alu.n
Select Alu repeats from REPBASE, suitable for masking Alu repeats from query sequences. It is available by anonymous FTP from ncbi.nlm.nih.gov (under the /pub/jmc/alu directory). See "Alu alert" by Claverie and Makalowski, Nature vol. 371, page 752 (1994).

env.nt

DNA sequence directly from the environment (ie. from all organisms mixed together)

month.nt, month.htgs, month.est_human, month.est_mouse, month.est_other, month.gss

[no longer available; NCBI has dropped support of month databases;  one can implement a search limited to entries from any time period using the "limit to Entrez query" option available in NetBlast and at the NCBI site, but not in command line Blast].

A rolling one month lookback on sequences entered into the respective divisions over the last 30 days.