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