BLAST search
Enter sequence below in FASTA format (Example)
The query sequence is filtered for low complexity regions by default.
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Descriptions & Alignments

Search Hints

This BLAST search is 'blastn' against the full-reading and 5'/3' end sequence set of the full-length cDNA collections.
A sequence in FASTA format begins with a single-line description, followed by lines of sequence data. The description line is distinguished from the sequence data by a greater-than (">") symbol in the first column. It is recommended that all lines of text be shorter than 80 characters in length.
An example sequence in FASTA format is:
>gi|532319|pir|TVFV2E|TVFV2E envelope protein
Sequences are expected to be represented in the standard IUB/IUPAC amino acid and nucleic acid codes, with these exceptions: lower-case letters are accepted and are mapped into upper-case; a single hyphen or dash can be used to represent a gap of indeterminate length; and in amino acid sequences, U and * are acceptable letters (see below). Before submitting a request, any numerical digits in the query sequence should either be removed or replaced by appropriate letter codes (e.g., N for unknown nucleic acid residue or X for unknown amino acid residue).
The nucleic acid codes supported are:
A adenosine R G A (purine) W A T (weak) N A G C T (any)
C cytidine Y T C (pyrimidine) B G T C - gap of indeterminate length
G guanine K G T (keto) D G A T
T thymidine M A C (amino) H A C T
U uridine S G C (strong) V G C A
For those programs that use amino acid query sequences (BLASTP and TBLASTN), the accepted amino acid codes are:
A alanine H histidine Q glutamine Y tyrosine
B aspartate or asparagine I isoleucine R arginine Z glutamate or glutamine
C cystine K lysine S serine X any
D aspartate L leucine T threonine * translation stop
E glutamate M methionine U selenocysteine - gap of indeterminate length
F phenylalanine N asparagine V valine
G glycine P proline W tryptophan
The server filters your query sequence for low compositional complexity regions by default. Low complexity regions commonly give spuriously high scores that reflect compositional bias rather than significant position-by- position alignment. Filtering can elminate these potentially confounding matches (e.g., hits against proline-rich regions or poly-A tails) from the blast reports, leaving regions whose blast statistics reflect the specificity of their pairwise alignment. Queries searched with the blastn program are filtered with DUST. Other programs use SEG.
Low complexity sequence found by a filter program is substituted using the letter "N" in nucleotide sequence (e.g., "NNNNNNNNNNNNN") and the letter "X" in protein sequences (e.g., "XXXXXXXXX"). Users may turn off filtering by using the "Filter" option on the "Advanced options for the BLAST server" page.

Reference for the DUST program

Tatusov, R. L. and D. J. Lipman, in preparation. Hancock, J. M. and J. S. Armstrong (1994). SIMPLE34: an improved and enhanced implementation for VAX and Sun computers of the SIMPLE algorithm for analysis of clustered repetitive motifs in nucleotide sequences. Comput Appl Biosci 10:67-70.

Reference for the SEG program

Wootton, J. C. and S. Federhen (1993). Statistics of local complexity in amino acid sequences and sequence databases. Computers in Chemistry 17:149-163. Wootton, J. C. and S. Federhen (1996). Analysis of compositionally biased regions in sequence databases. Methods in Enzymology 266: 554-571.

Reference for the role of filtering in search strategies

Altschul, S. F., M. S. Boguski, W. Gish, J. C. Wootton (1994). Issues in searching molecular sequence databases. Nat Genet 6: 119-129.
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.
The statistical significance threshold for reporting matches against database sequences; the default value is 1e-5, 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.
Restricts database sequences to the number specified for which high-scoring segment pairs (HSPs) are reported; the default limit is 5. If more database sequences than this happen to satisfy the statistical significance threshold for reporting, only the matches ascribed the greatest statistical significance are reported. (See parameter B in the BLAST Manual).


Restricts the number of short descriptions of matching sequences reported to the number specified; default limit is 5 descriptions. See also EXPECT.


Restricts database sequences to the number specified for which high-scoring segment pairs (HSPs) are reported; the default limit is 5. 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.
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