Blast Rule(00-03-09)

1.Choose entries with identity >= 95%(default) from the result of BLAST search. If user specified lower limit id, use it to choose entries.

Example)
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  sp|P00173|CYB5_RAT CYTOCHROME B5 >gi|65657|pir||CBRT5 cytochrome b5, microsomal -
         rat >gi|220730|dbj|BAA02492| (D13205) cytochrome b5
         precursor [Rattus rattus] >gi|2257957 (AF007108)
         cytochrome b5 [Rattus norvegicus]
         Length = 134

  Score = 198 bits (498), Expect = 7e-51
  Identities = 94/94 (100%), Positives = 94/94 (100%)

Query: 1 DKDVKYYTLEEIQKHKDSKSTWVILHHKVYDLTKFLEEHPGGEEVLREQAGGDATENFED 60
         DKDVKYYTLEEIQKHKDSKSTWVILHHKVYDLTKFLEEHPGGEEVLREQAGGDATENFED
Sbjct: 6 DKDVKYYTLEEIQKHKDSKSTWVILHHKVYDLTKFLEEHPGGEEVLREQAGGDATENFED 65

Query: 61 VGHSTDARELSKTYIIGELHPDDRSKIAKPSETL 94
          VGHSTDARELSKTYIIGELHPDDRSKIAKPSETL
Sbjct: 66 VGHSTDARELSKTYIIGELHPDDRSKIAKPSETL 99
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2. Pull out "real data" and "embedded data" from the entries chosen. (Embedded data gets same score, identities, positives, expect value as real data)

Example)
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    real data: sp|P00173|
embedded data: gi|65657|, pir||CBRT5, gi|220730|, dbj|BAA02492|, gi|2257957| 
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3. Make a loop inside the saveframe containing "_Mol_residue_sequence". List all of the pdb entries and top 5 of other database entries (based on the score value) sorted by database name.

Example)
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  loop_
       _Database_name
       _Database_accession_code
       _Database_entry_mol_name
       _Sequence_query_to_submitted_percentage
       _Sequence_subject_length
       _Sequence_identity
       _Sequence_positive
       _Sequence_homology_expectation_value

       SWISS-PROT P00173 "CYTOCHROME B5"   100%  94  100%  100%  7e-51
  stop_
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  a)_Database_name

       convert: gi and gb ------> GenBank
                pdb ------> PDB
                sp ------> SWISS-PROT
                pir ------> PIR
                emb ------> EMBL
                dbj ------> DBJ
 
  b)_Database_accession_code
                gi: gi|accession_code
                gb: gb|accession_code|locus
               pdb: pdb|accession_code|chain
                sp: sp|accession_code|entryname
               pir: pir||accession_code
               emb: emb|accession_code|locus
               dbj: dbj|accession_code|locus or
                    dbj||accession_code

  c)_Database_entry_mol_name
               pdb and embeded data: "?"
               others : first line or 
                        string before >gi 

  d)_Sequence_query_to_submitted_percentage
               (sequence query length / residue count) * 100
  e)_Sequence_subject_length
	       length value
  f)_Sequence_identity
               identity value
  g)_Sequence_positive (No positive tag for 'blastn')
               positive value
  h)_Sequence_homology_expectation_value
               Expect value

4. Update the time tags in front of the loop.

Example)
-----------------------------------------------------------------------------
   _Sequence_homology_query_date                2000-03-09
   _Sequence_homology_query_revisied_last_date  2000-03-02
-----------------------------------------------------------------------------

5. Make a loop inside the saveframe containing " _Mol_system_name" and list all pdb entries.

Example)
-----------------------------------------------------------------------------

   loop_
       _Database_name
       _Database_accession_code
       _Database_entry_mol_name
       _Database_entry_details

       PDB 1BFX ? .
       PDB 1IEU ? .
       PDB 1IET ? .
       PDB 1AQA ? .
       PDB 2AXX ? .
       PDB 1AW3 ? .
       PDB 1AXX ? .
       PDB 1B5A ? .
       PDB 1B5B ? .
       PDB 1BLV ? .
       PDB 1WDB ? .
       PDB 3B5C ? .
       PDB 1CYO ? .
   stop_
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