Program for search the homology of a processed sequence with sequences from PDB

The Fold program searches for the homologues of a processed sequence in the PDB with use of files specially prepared by envbc program, which contain the following fields for each position:
• Amino acid in three letter code
• Area Buried
• Fraction Polar
• Secondary structure assignment

Program selects 100 cases with maximal similarity properties.

Keys for program run string:
1. Name of a file containing the processed sequence in FASTA format with size of not more than 1000 nucleotides and with strings' length of not more than 80 positions. As such a file, the specially prepared file of alignments of the processed sequence with other ones that does not contain gaps in test sequence can be used (see example for SSPAL program).
2. Name of a file containing the secondary structure of the processed sequence (see description for SSPAL or PSSF output files).
3. Name of the output file containing the results of comparison in the following format:

   
   	T0234  165
       
   	1VL7A Sc_b= 34906.0 Sc_lg= 1393.7 l2= 135
   	1G79A Sc_b=  3770.0 Sc_lg=  139.5 l2= 199
   	1G76A Sc_b=  3755.0 Sc_lg=  138.9 l2= 199
   

   The first string contains the name and length of tested sequence, the following ones - names of PDB sequences, common and relevant homology scores, and lengths of PDB sequences.
4. Aligning mode: 'f' - Global, 'l' - Local.
5. Name of the output file containing the alignment of the processed sequence with most homologous PDB sequence of the following type:

   
   >T0283  112
   1ORJA Sc_b=  2385.0 Sc_lg=  104.5 l2= 126
            10        20        30        40        50        60
    aaaaaaaa     aaaaaaaaaaaaa  aaaaaaaaaaaaaa        aaaaaaaaaa
    MSFIEKMIGSLNDKREWKAMEARAKALPKEYHHAYKAIQKYMWTSGGPTDWQDTKRIFGG
    IECLERAIEIYDQVNELEKRKEFVENIDRVYD-IISALKSFLDHEKGKEIAKNLDTIYTI
    aaaaaaaaa       aaaaaaaaaaaaaaaa-aaaaaaa       aaaaaaaaaaaaa
            70        80        90       100
    aaaaaaaaaa         aaaaaaaaaaaaaaaaaaaaaaaaaa   
    ILDLFEEGAAEGKKVTDLTGEDVAAFCDELMKDTKTWMDKYRTKLNDS
    ILNTLV-----KV---DKTKEELQKIL-EILKDLREAWEEVKKKVHHH
    aaaaaa-----  ---   aaaaaaaa-aaaaaaaaaaaaaaaaaa 
   

6. Name of a file containing the list of PDB sequences. Choosing a single id from the list, user can make an alignment of processed sequence exactly to chosen sequence independently of their similarity degree.
7. The path to DB files. The last symbol - '/'.