BLAST Search main parameters

HISTOGRAM

Display a histogram of scores for each search; default is yes. (See parameter H in the BLAST Manual).

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 below), only the matches ascribed the greatest statistical significance are reported.

EXPECT

The statistical significance threshold for reporting matches against database sequences; the default value is 10, such that 10 matches are expected to be found merely by chance, according to the stochastic model of Karlin and Altschul (1990). If the EXPECT value of 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. Fractional values are acceptable.

CUTOFF

Cutoff score for reporting high-scoring segment pairs. The default value is calculated from the EXPECT value (see above). HSPs are reported for a database sequence only if the statistical significance ascribed to them is at least as high as would be ascribed to a lone HSP having a score equal to the CUTOFF value. Higher CUTOFF values are more stringent, leading to fewer chance matches being reported. (See parameter S in the BLAST Manual). Typically, significance thresholds can be more intuitively managed using EXPECT.

MATRIX

Specify an alternate scoring matrix for BLASTP, BLASTX, TBLASTN and TBLASTX. The default matrix is BLOSUM62 (Henikoff & Henikoff, 1992). The valid alternative choices include: PAM40, PAM120, PAM250 and IDENTITY. No alternate scoring matrices are available for BLASTN; specifying the MATRIX directive in BLASTN requests returns an error response.

STRAND

Restrict a TBLASTN search to just the top or bottom strand of the database sequences; or restrict a BLASTN, BLASTX or TBLASTX search to just reading frames on the top or bottom strand of the query sequence.

INCLUSION THRESHOLD

The statistical significance threshold for including a sequence in the model used by PSI-BLAST on the next iteration.

ORGANISM NAME

Enter the organism name in the form "Genus species" (e.g., "Homo sapiens"). A number of popular organism names are listed on a pull-down menu.

TAXONOMIC CLASSIFICATION

Enter any taxonomic group from the NCBI taxonomy (e.g. "Mammalia").

Some popular groups are:

Archaea
Bacteria
Eukaryota
Embryophyta (higher plants)
Fungi
Metazoa (multicellular animals)
Vertebrata
Mammalia
Rodentia
Primates

Explore the taxonomy database at NCBI

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 (Human repeats)

This option masks Human repeats (LINE's and SINE's) and is especially useful for human sequences that may contain these repeats. This option is still experimental and under development, so it may change in the near future.

FILTER (Mask for lookup table only)

This option masks only for purposes of constructing the lookup table used by BLAST. The BLAST extensions are performed without masking. This option is still experimental and may change in the near future.

NCBI-gi

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

Query Genetic Code

Genetic code to be used in blastx translation of the query.

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.

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