blastpgp arguments:
-d Database [String]
default = nr
-i Query File [File In]
default = stdin
-A Multiple Hits window size (zero for single hit algorithm) [Integer]
default = 40
-f Threshold for extending hits [Integer]
default = 0
-e Expectation value (E) [Real]
default = 10.0
-m alignment view options:
0 = pairwise,
1 = query-anchored showing identities,
2 = query-anchored no identities,
3 = flat query-anchored, show identities,
4 = flat query-anchored, no identities,
5 = query-anchored no identities and blunt ends,
6 = flat query-anchored, no identities and blunt ends,
7 = XML Blast output,
8 = Tabular output,
9 = Tabular output with comments [Integer]
default = 0
-o Output File for Alignment [File Out] Optional
default = stdout
-y Dropoff (X) for blast extensions in bits (default if zero) [Real]
default = 7.0
-P 0 for multiple hits 1-pass, 1 for single hit 1-pass, 2 for 2-pass [Integer]
default = 0
-F Filter query sequence with SEG [String]
default = F
-G Cost to open a gap [Integer]
default = 11
-E Cost to extend a gap [Integer]
default = 1
-X X dropoff value for gapped alignment (in bits) [Integer]
default = 15
-N Number of bits to trigger gapping [Real]
default = 22.0
-g Gapped [T/F]
default = T
-S Start of required region in query [Integer]
default = 1
-H End of required region in query (-1 indicates end of query) [Integer]
default = -1
-a Number of processors to use [Integer]
default = 1
-I Show GI's in deflines [T/F]
default = F
-h e-value threshold for inclusion in multipass model [Real]
default = 0.005
-c Constant in pseudocounts for multipass version [Integer]
default = 9
-j Maximum number of passes to use in multipass version [Integer]
default = 1
-J Believe the query defline [T/F]
default = F
-Z X dropoff value for final gapped alignment (in bits) [Integer]
default = 25
-O SeqAlign file ('Believe the query defline' must be TRUE) [File Out] Optional
-M Matrix [String]
default = BLOSUM62
-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
-C Output File for PSI-BLAST Checkpointing [File Out] Optional
-R Input File for PSI-BLAST Restart [File In] Optional
-W Word size, default if zero [Integer]
default = 0
-z Effective length of the database (use zero for the real size) [Real]
default = 0
-K Number of best hits from a region to keep [Integer]
default = 0
-s Compute locally optimal Smith-Waterman alignments [T/F]
default = F
-Y Effective length of the search space (use zero for the real size) [Real]
default = 0
-p program option for PHI-BLAST [String]
default = blastpgp
-k Hit File for PHI-BLAST [File In]
default = hit_file
-T Produce HTML output [T/F]
default = F
-Q Output File for PSI-BLAST Matrix in ASCII [File Out] Optional
-B Input Alignment File for PSI-BLAST Restart [File In] Optional
-l Restrict search of database to list of GI's [String] Optional
-U Use lower case filtering of FASTA sequence [T/F] Optional
default = F
-t Use composition based statistics [T/F]
default = T
-L Cost to decline alignment (disabled when 0) [Integer]
default = 0
