genoma.unsam.edu.ar :: blast :: documentation

BLAST Documentation and tutorials

blastall arguments

If you know what you're doing, you can pass any of these arguments as extra options ('Add extra options to blastall?')

  -p  Program Name [String]
  -d  Database [String]
      default = nr
  -i  Query File [File In]
      default = stdin
  -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 = tab-delimited fields [Integer]
    default = 0
  -o  BLAST report Output File [File Out]  Optional
      default = stdout
  -F  Filter query sequence (DUST with blastn, SEG with others) [String]
      default = T
  -G  Cost to open a gap (zero invokes default behavior) [Integer]
      default = 0
  -E  Cost to extend a gap (zero invokes default behavior) [Integer]
      default = 0
  -X  X dropoff value for gapped alignment (in bits) (zero invokes default
	    behavior) [Integer]
      default = 0
  -I  Show GI's in deflines [T/F]
      default = F
  -q  Penalty for a nucleotide mismatch (blastn only) [Integer]
      default = -3
  -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  Perfom gapped alignment (not available with tblastx) [T/F]
      default = T
  -Q  Query Genetic code to use [Integer]
      default = 1
  -D  DB Genetic code (for tblast[nx] only) [Integer]
      default = 1
  -a  Number of processors to use [Integer]
      default = 1
  -O  SeqAlign file [File Out]  Optional
  -J  Believe the query defline [T/F]
      default = F
  -M  Matrix [String]
      default = BLOSUM62
  -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 (off by default, if used
	    a value of 100 is recommended) [Integer]
      default = 0
  -P  0 for multiple hits 1-pass, 1 for single hit 1-pass, 2 for 2-pass
	   [Integer]
      default = 0
  -Y  Effective length of the search space (use zero for the real size) [Real]
      default = 0
  -S  Query strands to search against database (for blast[nx], and tblastx).
	    3 is both, 1 is top, 2 is bottom [Integer]
      default = 3
  -T  Produce HTML output [T/F]
      default = F
  -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
  -y  Dropoff (X) for blast extensions in bits (0.0 invokes default behavior)
	    [Real]
      default = 0.0
  -Z  X dropoff value for final gapped alignment (in bits) [Integer]
      default = 0
  -R  PSI-TBLASTN checkpoint file [File In]  Optional
  -n  MegaBlast search [T/F]
      default = F
  -L  Location on query sequence [String]  Optional
  -A  Multiple Hits window size (zero for single hit algorithm) [Integer]
      default = 40
				

This is mainly a collection of links containing documentation and tutorials on BLAST, similarity searching and related topics. Suggestions/corrections are welcome: fernan@iib.unsam.edu.ar