KAIKOBLAST System


Databases for use with BLAST

---------------------------
The following databases are currently or future available
for BLAST searches:
    SW-WGS-RAMEN-CONTIGS        Silkworm (p50, 'Daizo' strain) whole genome shotgun (WGS), Ramen assemble contigs
    SW-CDNA-PARTIAL-ALL         Silkworm cDNA partial sequences from KAIKOcDNA database
    SW-CDNA-PARTIAL-CLUST       Silkworm cDNA partial sequences (clustered) from KAIKOcDNA database




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 against a protein sequence database
tblastn - Comparing a protein query sequence against a nucleotide 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 and JAPIO databases.




Parameters

---------------------

  program

     Specify the search program. Choose one of the following programs.
          blastn | blastp | blastx | tblastn | tblastx
     No default, YOU CANNOT OMIT THIS OPTION.

     Please confer "Available search programs" section.


  datalib

     Specify the databases in which homologous sequences are searched.
     Choose from following databases.
      SW-CDNA-PARTIAL-ALL | SW-CDNA-PARTIAL-CLUST
      SW-WGS-RAMEN-CONTIGS

     No default, YOU CANNOT OMIT THIS OPTION.

     Please confer "Databases for use with BLAST" section.



  wordsize

     Specify the word size. You had better not change the wordsize 
     other than 11 for blastn.                                  [integer]
     Default value: blastn=11, others=3

                 Maximum  Minimum
          -----------------------
          blastn   14        7
          others    4        2



  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
          7 = XML Blast output
     Default value: 0



  filter

     Specify the filter query sequence (DUST with blastn, SEG with others).
     SEG program is for identifying and masking segments of low compositional
     complexity in amino acid sequences.                        [T/F]
     Default value: T



  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  (not available with tblastx)

     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
NIAS DNA Bank