Descriptions
View original
BLAST documentation at NCBI.
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Use of Sequence Data
The sequences are confidential. In case you wish to
use the data in a publication, please contact
us beforehand.
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Query Sequence
Enter your sequence as plain text or in fastA format.
For the BLAST
methods BLASTN and TBLASTX the query sequence should be nucleotide,
for the BLAST method TBLASTN you should enter a protein sequence.
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Mask nt Query Sequence
You may choose to mask the query sequence at repetitive and
low-complexity regions. Currently, this is done with RepeatMasker (Smit,AFA & Green,P).
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BLAST method
This interface uses the BLAST program palette developed at
WashU.
| - auto - | |
automatically chooses the right program according to the detected query
sequence type and sequence type of the selected BLAST database. Only
TBLASTX has to be set manually.
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| BLASTN | |
compares a nucleotide query sequence against the entries in a
nucleotide sequence database
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| TBLASTX | |
compares the all-frame translations
of a nucleotide query sequence against the all-frame
translations of the entries in a nucleotide sequence database
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| TBLASTN | |
compares a protein query sequence against the all-frame translations
of the entries in a nucleotide sequence database
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Databases
| Alexandrium minutum EST | | 4320 ESTs from Alexandrium minutum |
| Fibrocapsa japonica EST | | 5162 ESTs from Fibrocapsa japonica |
| Prymnesium parvum EST | | 6381 ESTs from Prymnesium parvum |
| Pseudo-nitzschia multistriata EST | | 4667 ESTs from Pseudo-nitzschia multistriata |
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Mask Low-Complexity Regions
Setting this switch the program masks the query sequence for low-complexity
regions. The masking is done with the program 'RepeatMasker'
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Expect Threshold
The statistical significance threshold for reporting
matches against database sequences. The expect value
given for each HSP in the BLAST report specifies
the expectancy value for the number of database
entries 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 higher 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.
Though you may extend the number of matching database entries
by rising the expect threshold the maximum total number of entries
that's reported is restricted to 120 (the best matching entries
are displayed). Beside that, the threshold value is restricted to
a maximum of 5.0e-4. A higher value won't add any meaningful hit
to your search result (believe it).
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Literature
Altschul, Stephen F., Warren Gish, Webb Miller, Eugene W. Myers,
and David J. Lipman. Basic local alignment
search tool. J. Mol. Biol. 215, 403-410 (1990).
Karlin, Samuel and Stephen F. Altschul (1990). Methods for
assessing the statistical significance of molecular sequence
features by using general scoring schemes. Proc. Natl. Acad.
Sci. USA 87:2264-68.
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