Bioinformatics and Functional Genomics

Table 4-1. Protein sequence databases that can be searched by standard BLAST searching (modified from http://www.ncbi.nlm.nih.gov/blast/html/blastcgihelp.html#protein_databases).

Database	Description
Nr	Non-redundant GenBank coding sequences & PDB & SwissProt & PIR & PRF
Month	Sequence data released in the previous 30 days
Swissprot	Most recent release from SwissProt
Drosophila	Drosophila proteins from the Drosophila Genome Project (http://www.fruitfly.org)
S. cerevisiae	Saccharomyces cerevisiae (yeast) proteins
Ecoli	Escherichia coli proteins
Pdb	Protein data bank at Brookhaven (http://www.rcsb.org/pdb/)
alu	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).

 

Table 4-2. Nucleotide sequence databases that can be searched by standard BLAST searching (modified from http://www.ncbi.nlm.nih.gov/blast/html/blastcgihelp.html#nucleotide_databases).

Database	Description
nr	All GenBank+EMBL+DDBJ+PDB sequences (but no EST, STS, GSS, or phase 0, 1 or 2 HTGS sequences). No longer "non-redundant."
Month	All new or revised GenBank+EMBL+DDBJ+PDB sequences released in the last 30 days.
Drosophila genome	Drosophila genome provided by Celera and Berkeley Drosophila Genome Project (BDGP)(http://www.fruitfly.org/).
Dbest	Database of GenBank+EMBL+DDBJ sequences from EST Divisions
Dbsts	Database of GenBank+EMBL+DDBJ sequences from STS Divisions
Htgs	Unfinished High Throughput Genomic Sequences
Gss	Genome Survey Sequence, includes single-pass genomic data, exon-trapped sequences, and Alu PCR sequences.
S. cerevisiae	Yeast (Saccharomyces cerevisiae) genomic nucleotide sequences
E. coli	Escherichia coli genomic nucleotide sequences
Pdb	Sequences derived from the 3-dimensional structure from Brookhaven Protein Data Bank (http://www.rcsb.org/pdb/)
Vector	Vector subset of GenBank(R), NCBI, in ftp://ncbi.nlm.nih.gov/blast/db/
Mito	Database of mitochondrial sequences
alu	Select Alu repeats from REPBASE, suitable for masking Alu repeats from query sequences (available by anonymous FTP from ncbi.nlm.nih.gov under the /pub/jmc/alu directory).
epd	Eukaryotic Promotor Database (http://www.genome.ad.jp/dbget-bin/www_bfind?epd)

 

Table 4-3. The effect of changing the threshold values on a blastp search. These three searches were done using the NCBI blastcl3 program (NetBLAST) using retinol-binding protein 4 (NP_006735) as a query. When the threshold parameter (f) was changed to 5 there were over 2 billion hits and 589 million extensions, ultimately producing more gapped HSPs (146) than found with the higher threshold value of 17.

	f=11 (default)	f=5	f=17
Number of sequences in database	1,046,476	1,046,476	1,046,476
Number of hits to database	129,839,417	2,200,945,350	12,002,487
Number of extensions	5,198,652	589,935,555	61,838
Number of successful extensions	8,377	13,145	1,117
Number of HSP's gapped	145	146	93

 

Table 4-4. The relationship of E values to P values in BLAST, using Equation 4-8. Small E values (0.05 or less) correspond closely to the P values.

E value	P value
10	0.99995460
5	0.99326205
2	0.86466472
1	0.63212056
0.1	0.09516258
0.05	0.04877058
0.001	0.0009995
0.0001	0.0001000