GeneBee BLAST 2.2.8 Services Help

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Databases available for BLAST search (More info)

The BLAST pages offer several different databases for searching.

Peptide Sequence Databases

Nucleotide Sequence Databases

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Limit by Entrez Query

BLAST searches can be limited to the results of an Entrez query against the database chosen. This can be used to limit searches to subsets of the BLAST databases. Any terms can be entered that would normally be allowed in an Entrez search session. For example:
protease NOT hiv1[Organism] 
This will limit a BLAST search to all proteases, except those in HIV 1. This can also be used to limit searches to a particular molecule type:
biomol_mrna[PROP] AND brain
To limit to a specific organism you can enter the name of the organism in the Entrez Query field with the [Organism] qualifier. For example:
Mus musculus[Organism]
For help in constructing Entrez queries please see the " Writing Advanced Search Statements" section of the Entrez Help document.

Filter (Low-complexity)

Mask off segments of the query sequence that have low compositional complexity, as determined by the SEG program of Wootton & Federhen (Computers and Chemistry, 1993) or, for BLASTN, by the DUST program of Tatusov and Lipman (in preparation). Filtering can eliminate statistically significant but biologically uninteresting reports from the blast output (e.g., hits against common acidic-, basic- or proline-rich regions), leaving the more biologically interesting regions of the query sequence available for specific matching against database sequences.

Filtering is only applied to the query sequence (or its translation products), not to database sequences. Default filtering is DUST for BLASTN, SEG for other programs.

It is not unusual for nothing at all to be masked by SEG, when applied to sequences in SWISS-PROT, so filtering should not be expected to always yield an effect. Furthermore, in some cases, sequences are masked in their entirety, indicating that the statistical significance of any matches reported against the unfiltered query sequence should be suspect.

Filter (Mask lower case)

This option specifies that any lower-case letters in the input FASTA file should be masked.

Expect

The statistical significance threshold for reporting matches against database sequences; the default value is 10, meaning that 10 matches are expected to be found merely by chance, according to the stochastic model of Karlin and Altschul (1990). If the statistical significance ascribed to a match is greater than the EXPECT threshold, the match will not be reported. Lower EXPECT thresholds are more stringent, leading to fewer chance matches being reported. Increasing the threshold shows less stringent matches. Fractional values are acceptable.

Word size

The BLAST algorithm uses "words" to nucleate regions of similarity. The default Word size for a protein sequence is 3 residues and for nucleotide sequences it is 11 bp. A blastn search will not work with a Word size of less than 7. A good rule of thumb is that the query length must be at least twice the Word size. For example, if your query is a protein sequence of 4 residues, than the Word size should be reduced to 2. Please note that the smaller the Word size, the slower your search will be.

Nucleotide mismatch penalty

Penalty for nucleotide mismatch. For blastn and megablast programs only. Default value is -3.

Matrix

A key element in evaluating the quality of a pairwise sequence alignment is the "substitution matrix", which assigns a score for aligning any possible pair of residues. The theory of amino acid substitution matrices is described in [1], and applied to DNA sequence comparison in [2]. In general, different substitution matrices are tailored to detecting similarities among sequences that are diverged by differing degrees [1-3]. A single matrix may nevertheless be reasonably efficient over a relatively broad range of evolutionary change [1-3]. Experimentation has shown that the BLOSUM-62 matrix [4] is among the best for detecting most weak protein similarities. For particularly long and weak alignments, the BLOSUM-45 matrix may prove superior. A detailed statistical theory for gapped alignments has not been developed, and the best gap costs to use with a given substitution matrix are determined empirically. For proteins, a provisional table of recommended substitution matrices and gap costs for various query lengths is:
Query length Substitution matrix Gap costs
<35 PAM30 (9,1)
35-50 PAM70 (10,1)
50-80 BLOSUM80 (10,1)
>85 BLOSUM62 (11,1)

Open And Extended Gaps

The raw score of an alignment is the sum of the scores for aligning pairs of residues and the scores for gaps. Gapped BLAST and PSI-BLAST use "affine gap costs" which charge the score -a for the existence of a gap, and the score -b for each residue in the gap. Thus a gap of k residues receives a total score of -(a+bk); specifically, a gap of length 1 receives the score -(a+b). Only following combinations of the Matrix, Open & Extended Gaps are available: Recomended combinations are colored.
BLOSUM80 BLOSUM62
Open
Gap
Extended
Gap
Open
Gap
Extended
Gap
Open
Gap
Extended
Gap
Open
Gap
Extended
Gap
11 1 8 2 12 1 9 2
10 1 7 2 11 1 8 2
9 1 6 2 10 1 7 2

BLOSUM50 BLOSUM45
Open
Gap
Extended
Gap
Open
Gap
Extended
Gap
Open
Gap
Extended
Gap
Open
Gap
Extended
Gap
Open
Gap
Extended
Gap
Open
Gap
Extended
Gap
18 1 15 2 12 3 19 1 15 2 13 3
17 1 14 2 11 3 18 1 14 2 12 3
16 1 13 2 10 3 17 1 13 2 11 3
15 1 12 2 9 3 16 1 12 2 10 3

PAM30 PAM70
Open
Gap
Extended
Gap
Open
Gap
Extended
Gap
Open
Gap
Extended
Gap
Open
Gap
Extended
Gap
10 1 7 2 11 1 8 2
9 1 6 2 10 1 7 2
8 1 5 2 9 1 6 2

Drop Off

Dropoff value for gapped alignment ( in bits ). Default value is zero.

Other Advanced Options

Options Valuetype Default Descriptions
-r Integer 1 Reward for a nucleotide match
-f Integer 0 Threshold for extending hits, default if zero
-Q Integer 1 Query Genetic code to use
-D Integer 1 DB Genetic code (for tblast[nx] only)
-J T/F F Believe the query defline
-W Integer 0 Word size, default if zero
-z Integer 0 Effective length of the database (use zero for the real size)
-K Integer 100 Number of best hits from a region to keep
-L Integer 20 Length of region used to judge hits
-Y Real 0 Effective length of the search space (use zero for the real size)

NCBI GI's

Causes NCBI gi identifiers to be shown in the output, in addition to the accession and/or locus name.

HTML Output

Causes output to be shown in PLAIN or HTML format.

Graphical Overview

An overview of the database sequences aligned to the query sequence is shown. The score of each alignment is indicated by one of five different colors, which divides the range of scores into five groups. Multiple alignments on the same database sequence are connected by a striped line. Mousing over a hit sequence causes the definition and score to be shown in the window at the top, clicking on a hit sequence takes the user to the associated alignments.

Descriptions

Restricts the number of short descriptions of matching sequences reported to the number specified; default limit is 100 descriptions. See also EXPECT.

Alignments

Restricts database sequences to the number specified for which high-scoring segment pairs (HSPs) are reported; the default limit is 100. If more database sequences than this happen to satisfy the statistical significance threshold for reporting (see EXPECT), only the matches ascribed the greatest statistical significance are reported.

Alignment View

Level Of Details in Alignment Output

Choose how many details are to be shown in the output.

Genetic Codes

The parameter D can be set to a positive integer to select the genetic code that will be used by blastx and tblastx to translate the query sequence. In each case, the default genetic code is the so-called "Standard" or "Universal" genetic code. Note: the numerical identifiers used here for genetic codes parallel those defined in the NCBI software Toolbox; hence some numerical values will be skipped as genetic codes are updated.

The list of genetic codes available and their associated values for the parameter D are:

Value Description
1 Standard or Universal
2 Vertebrate Mitochondrial
3 Yeast Mitochondrial
4 Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma
5 Invertebrate Mitochondrial
6 Ciliate Macronuclear
9 Echinodermate Mitochondrial
10 Alternative Ciliate Macronuclear
11 Eubacterial
12 Alternative Yeast
13 Ascidian Mitochondrial
14 Flatworm Mitochondrial