Available search programs
-------------------------
blastn  - Comparing a nucleotide query sequence
             against a nucleotide sequence database.
blastp  - Comparing an amino acid query sequence
             against a protein sequence database.
blastx  - Comparing a nucleotide query sequence translated
             in all reading frames aginst a protein sequence database.
tblastn - Comparing a protein query sequence aginst a nucleocide sequence
             database dynamically translated in all reading frames.
tblastx - Comparing the six-frame translations of a nucleotide query
             sequence against the six-frame translations of a nucleotide
             sequence database.
          Please note that tblastx program cannot be used with the DNA,
             DDBJ, EMBL, GENBANK, JAPIO and CODON databases.

Parameters

  descriptions
     Specify the number of one-line descriptions.               [integer]
     Default value: 100

  alignments
     Specify the number of alignments to show.                  [integer]
     Default value: 100

  expect
     Specify the expected number of homologous sequences
     in the database.  If you need to get more sequences
     with lower homology score, increase the "expect" value. 
     If you need only sequences with very high homology scores,
     decrease the value.                                        [Real]
     Default value: 10.0

 
  match  (blastn only)
     Specify the reward for a nucleotide match.                 [integer]
     Default value: 1

  mismatch  (blastn only)
     Specify the penalty for a nucleotide mismatch.             [integer]
     Default value: -3

  view
     Specify the alignment view options.
     View parameter table:
          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
     Default value: 0

  filter
       The server filters your query sequence for low compositional complexity 
     regions by default. Low complexity regions commonly give spuriously high 
     scores that reflect compositional bias rather than significant position-by- position 
     alignment. Filtering can elminate these potentially confounding matches 
     (e.g., hits against proline-rich regions or poly-A tails) from the blast reports, 
     leaving regions whose blast statistics reflect the specificity of their pairwise 
     alignment. Queries searched with the blastn program are filtered with DUST. Other 
     programs use SEG. 
       Low complexity sequence found by a filter program is substituted using the 
     letter "N" in nucleotide sequence (e.g., "NNNNNNNNNNNNN") and the letter "X" 
     in protein sequences (e.g., "XXXXXXXXX"). 

  gap_open
     Specify the cost to open a gap
                (zero invokes default behavior).                [Integer]
     Default value: blastn = 5, others = See "gap_extend"

  gap_extend
     Specify the cost to extend a gap
                (zero invokes default behavior).                [Integer]
     Default value: blastn = 2, others = See the following

     Sets of gap_open and gap_extend values (except blastn):
          gap_open   gap_extend
          ---------------------
             11         1(default)
             10         1
              9         2
              8         2

  dropoff
     Specify X dropoff value for gapped alignment (in bits)
                (zero invokes default behavior).                [integer]
     Default value: 0

  gi
     Specify GI's in deflines.                                  [T/F]
     Default value: F

  extend_hit
     Specify the threshold for extending hits.                  [integer]
     Default value: 0

  gap_align
     Perform gapped alignment                                   [T/F]
     Default value: T

  query_code  (blastx only)
     Specify Query Genetic code to be used in blastx translation
     of the query. 
     Query genetic code table:
           1 = Standard
           2 = Vertebrate Mitochondrial
           3 = Yeast Mitochondrial
           4 = Mold Mitochondrial
           5 = Invertebrate Mitochondrial
           6 = Ciliate Macronuclear
           9 = Echinodermate Mitochondrial
          10 = Euplotid Nuclear
          11 = Bacterial
          12 = Alternative Yeast Nuclear
          13 = Ascidian Mitochondrial
          14 = Flatworm Mitochondrial
          15 = Blepharisma Macronuclear
     Default value: 1