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:
-
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).
- Name of a file containing the secondary structure
of the processed sequence (see description for SSPAL or PSSF output files).
- 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.
- Aligning mode: 'f' - Global, 'l' - Local.
- 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
- 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.
- The path to DB files. The last symbol - '/'.