MonarchBase - Migratory

blastall 2.2.24 arguments:

-p Program Name
-d Database
-e Expectation value (E) [Real]
    default = 1e-5
-F Filter query sequence (DUST with blastn, SEG with others) [String]
    default = T
-G Cost to open a gap (-1 invokes default behavior) [Integer]
    default = -1
-E Cost to extend a gap (-1 invokes default behavior) [Integer]
    default = -1
-q Penalty for a nucleotide mismatch (blastn only) [Integer]
    default = -3
-r Reward for a nucleotide match (blastn only) [Integer]
    default = 1
-v Number of database sequences to show one-line descriptions for (V) [Integer]
    default = 500
-b Number of database sequence to show alignments for (B) [Integer]
    default = 250
-g Perform gapped alignment (not available with tblastx) [T/F]
    default = T
-M Matrix [String]
    default = BLOSUM62
-U Use lower case filtering of FASTA sequence [T/F] Optional
-n MegaBlast search [T/F]
    default = F