BLAST parameters

Expect threshold

The expect threshold (E value) is the maximum expect value required for a hit to be returned. The expect threshold is the statistical significance threshold for reporting matches against database sequences. If the statistical significance ascribed to a match is greater than the expect threshold, the match will not be reported. Lower expect threshold values are more stringent, leading to fewer chance matches being reported (source: http://www.ncbi.nlm.nih.gov/blast/blast_help.shtml [external website]).

Maximum number of alignments

Select the number of target sequences to display in the results. Choosing fewer sequences produces results faster.

BLAST filter

Filtering is on by default and filters the query sequence for low complexity regions. In a protein search low complexity regions appear as 'X's in the alignment while in a nucleotide search they appear as 'N's. The score and E value of a match may be affected by filtering since it effectively shortens the query length.

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