Availability
PSI-BLAST is installed on all cluster nodes in /usr/local/bin.
Command line tips
The syntax to call blastpgp is as follows:
blastpgp 2.2.11 arguments:
-d Database [String] default = nr -i Query File (not needed if restarting from scoremat) [File In] Optional default = stdin -A Multiple Hits window size [Integer] default = 40 -f Threshold for extending hits [Integer] default = 11 -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 10 = ASN, text 11 = ASN, binary [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 hit, 1 for single hit [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 = 0.002
-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 [Integer]
default = 3
-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
0 or F or f: no composition-based statistics 1 or T or t: Composition-based statistics as in NAR 29:2994--3005, 2001 2: Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, conditioned on sequence properties in round 1 3: Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, unconditionally in round 1
[String] default = 1 -q ASN.1 Scoremat input of checkpoint data:
0: no scoremat input 1: Restart is from ASCII scoremat checkpoint file, 2: Restart is from binary scoremat checkpoint file [Integer] Optional
default = 0 -u ASN.1 Scoremat output of checkpoint data:
0: no scoremat output 1: Output is ASCII scoremat checkpoint file (requires -J), 2: Output is binary scoremat checkpoint file (requires -J) [Integer] Optional
default = 0 -L Cost to decline alignment (disabled when 0) [Integer] default = 0