ProtrepeatsDB : BLAST

BLAST against ProtRepeatsDB

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Target database:

Database to search:

Input sequence:

Enter an amino acid query sequence. The sequence may include a FASTA-style definition line. Any other line numbers or
whitespace will be removed.

for example: FHKILTNTDPNDEVERRNADNKEDLTSADPEGQIMREYAADPEYRKHLEI

Only for short sequence BLAST:
Run short sequence BLAST    Shortseq Default Parameters: (W=2, E=20000, Matrix=PAM30 & filter=Off)
        To Blast short sequence with your own parameters, keep 'Shortseq Params' unselected, ELSE checked.

BLAST program:

BLAST program:

Note that WU-BLAST and NCBI-BLAST are two different implementations of the BLAST algorithm; they should behave
similarly but will exhibit some differences.

Run (additional parameters below)

BLAST parameters:

Expect value (E):

Alignment View (A):
(For NCBI-Blast only)

Substitution matrix:
(Wu: For WuBlast only)

Limit BLAST output:

Maximum Descriptions (V):

Maximum Alignments (B):

Run

Help

BLAST parameters:

BLAST 'E' option

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). However, here the dafault E value is kept as 1000 to perform short sequence Blast. 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. (See parameter E in the BLAST Manual).

BLAST 'm' option

The alignment output can be viewed according to the option selected. The default option is pairwise alignment.

BLAST substitution matrix

Select a substitution matrix to be used. Note that the matrices listed are only appropriate for queries involving proteins or translated DNA sequences.

Limit BLAST output:

BLAST 'V' option

Restricts the number of short descriptions of matching sequences reported to the number specified; default limit is 100 descriptions. (See parameter V in the manual page). See also EXPECT and CUTOFF.

BLAST 'B' option

Restricts database sequences to the number specified for which high-scoring segment pairs (HSPs) are reported; the default limit is 50. If more database sequences than this happen to satisfy the statistical significance threshold for reporting (see EXPECT and CUTOFF below), only the matches ascribed the greatest statistical significance are reported. (See parameter B in the BLAST Manual).

Limit BLAST to short sequnces:

To perform short sequence BLAST, select the "Run short sequence BLAST" box and by default, the parameters of (Word size=2, Evalue=1000, Matrix=PAM30 and Filter=off) will be used. For selecting parameters other than that of default, uncheck the "Shortseq Params" option and choose the values accordingly down the form.