GridBlast -p <blast_executable_name> -d <database_name> <OPTIONS>

Command Line Options

• GridBlast Options
  
  --help
  
  Provides directions to access the man pages.
  
  --version
  
  This option used along with the GridBlast.pl command prints the current version of GridBlast.
  
  -p Program Name [String]
  
  -d Database [String] default = nr
  
  --resultsdir directory path
  
  This option allows the user to specify the directory name in which to put the results. This option HAS to be supplied for the program to work.
  
  --datadir directory path
  
  This option allows the user to specify the directory path from which to get the database files. This option HAS to be supplied for the program to work.
  
  --format
  
  This option must be used along with unformatted database files. Unformatted database files must be stored in the format <name>.tar.Z whereas formatted databases must be stored as <name>.tar.gz
  
  --splitfile <filename>
  
  This option allows one to input a file containing multiple queries in fasta format. The file splitquery.pl provided along with the package will split this file into different queries and put them in the appropriate directories. =item
  
  --minmax This option uses the Minmax scheduler instead of the default proportional scheduler. Currently, the parameters required by minmax.c need to be entered manually and the program compiled. Future versions will do this automatically.
  
  --splitdb
  
  This option allows the users to split the database into as many partitions as the number of nodes. This is particularly useful for a grid environment where the bandwidths are low.
  
  --log
  
  This option allows the user to log information about the execution times for the various nodes as well as sundry other information during the execution of the program. The information is logged in GridBlast.log in the directory from which GridBlast was invoked.



• BLAST Options
  
  The only difference here is that all the Upper Case options for blastall have now been changed to a double letter. For e.g., blastall option -A has been changed to -AA.
  
  -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,
  
  9 tabular with comment lines [Integer]
  
  default = 0
  
  -FF Filter query sequence (DUST with blastn, SEG with others) [String] default = T
  
  -GG Cost to open a gap (zero invokes default behavior) [Integer] default = 0
  
  -EE Cost to extend a gap (zero invokes default behavior) [Integer] default = 0
  
  -XX X dropoff value for gapped alignment (in bits) (zero invokes default behavior) [Integer] default = 0
  
  -II Show GI's in deflines [T/F] default = F
  
  -q Penalty for a nucleotide mismatch (blastn only) [Integer] default = -3 =item
  
  -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
  
  -f Threshold for extending hits, default if zero [Integer] default = 0
  
  -g Perform gapped alignment (not available with tblastx) [T/F] default = T =item
  
  -QQ Query Genetic code to use [Integer] default = 1
  
  -DD DB Genetic code (for tblast[nx] only) [Integer] default = 1
  
  -a Number of processors to use [Integer] default = 1
  
  -OO SeqAlign file [File Out] Optional
  
  -JJ Believe the query defline [T/F] default = F
  
  -MM Matrix [String] default = BLOSUM62
  
  -WW Word size, default if zero [Integer] default = 0
  
  -z Effective length of the database (use zero for the real size) [String] default = 0
  
  -KK Number of best hits from a region to keep (off by default, if used a value of 100 is recommended) [Integer] default = 0
  
  -PP 0 for multiple hits 1-pass, 1 for single hit 1-pass, 2 for 2-pass [Integer] default = 0
  
  -YY Effective length of the search space (use zero for the real size) [Real] default = 0
  
  -SS Query strands to search against database (for blast[nx], and tblastx). 3 is both, 1 is top, 2 is bottom [Integer] default = 3
  
  -TT Produce HTML output [T/F] default = F
  
  -l Restrict search of database to list of GI's [String] Optional
  
  -UU Use lower case filtering of FASTA sequence [T/F] Optional default = F
  
  -y Dropoff (X) for blast extensions in bits (0.0 invokes default behavior) [Real] default = 0.0
  
  -ZZ X dropoff value for final gapped alignment (in bits) [Integer] default = 0
  
  -RR PSI-TBLASTN checkpoint file [File In] Optional
  
  -n MegaBlast search [T/F] default = F
  
  -LL Location on query sequence [String] Optional
  
  -AA Multiple Hits window size (zero for single hit algorithm) [Integer] default = 40