Manpage for psiblast

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 = 11
  -e  Expectation value (E) [Real]
    default = 10.0
  -m  alignment view options:
0 = pairwise,
1 = master-slave showing identities,
2 = master-slave no identities,
3 = flat master-slave, show identities,
4 = flat master-slave, no identities,
5 = master-slave no identities and blunt ends,
6 = flat master-slave, no identities and blunt ends [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 = 0.001
  -c  Constant in pseudocounts for multipass version [Integer]
    default = 10
  -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 one-line descriptions (V) [Integer]
    default = 500
  -b  Number of alignments to show (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) [Integer]
    default = 0
  -K  Number of best hits from a region to keep [Integer]
    default = 0
  -L  Length of region used to judge hits [Integer]
    default = 20
  -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