blast/docs/newoptions.html
<TITLE>BLAST search main parameters</TITLE>
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<h1>BLAST Search main parameters</h1>
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<p>
<dl>
<dt><b><a name = descriptions>DESCRIPTIONS</a></b>
<dd>Restricts the number of short descriptions of matching
sequences reported to the number specified; default
limit is 100 descriptions. See also EXPECT.
<dt><b><a name = alignments>ALIGNMENTS</a></b>
<dd>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.
<dt><b><a name = expect>EXPECT</a></b>
<dd>
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 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. Fractional
values are acceptable.
<dt><b><a name = inclusion>INCLUSION THRESHOLD</a></b>
<dd>
The statistical significance threshold for including a sequence
in the model used by PSI-BLAST on the next iteration.
<dt><b><a name = organism>ORGANISM NAME</a></b>
<dd>
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.
<dt><b><a name = taxonomic>TAXONOMIC CLASSIFICATION</a></b>
<dd>
Enter any taxonomic group from the NCBI taxonomy (e.g. "Mammalia").
<PRE>
Some popular groups are:
Archaea
Bacteria
Eukaryota
Embryophyta (higher plants)
Fungi
Metazoa (multicellular animals)
Vertebrata
Mammalia
Rodentia
Primates
</PRE>
<P>
<A HREF="/Taxonomy/tax.html">Explore the taxonomy database at NCBI</A>
<dt><b><a name = filter>FILTER (Low-complexity)</a></b>
<dd>
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. <BR>
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. <BR>
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.
<dt><b><a name = filter>FILTER (Human repeats)</a></b>
<dd>
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.<BR>
<dt><b><a name = filter>FILTER (Mask for lookup table only)</a></b>
<dd>
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.
<dt><b><a name = ncbi-gi>NCBI-gi<a></b>
<dd>
Causes NCBI gi identifiers to be shown in the output,
in addition to the accession and/or locus name.
<dt><b><a name = gencodes>Query Genetic Code<a></b>
<dd>
Genetic code to be used in blastx translation of the query.
<dt><b><a name = graphical-overview>Graphical Overview<a></b>
<dd>
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.
<FONT color=red>Mousing over</FONT> a hit sequence
causes the definition and score to be shown in the
window at the top, <FONT color=red>clicking</FONT> on a hit sequence takes the user to
the associated alignments.
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