siggen parses a multiple structure alignment generated by the EMBOSS application scopalign and corresponding files of residue contact data generated by the EMBOSS application contacts and generates a protein signature of a specified sparsity.

Here is a sample session with siggen:

% siggen
Generates a sparse protein signature
Location of alignment files for input [./]: ./jontest
Extension of alignment files for input [.align]:
Location of contact files for input [./]: ./jontest
Extension of contact files [.con]:
% sparsity of signature [10]:
Generate a randomized signature [N]:
Substitution matrix to be used [./EBLOSUM62]:
Score alignment on basis of residue conservation [Y]:
Score alignment on basis of number of contacts [Y]:
Score alignment on basis of conservation of contacts [Y]: N
Score alignment on a combined measure of number and conservation of contacts [N]:
Ignore alignment postitions with post_similar value of 0 [Y]:
Name of signature file for output [sig.sig]:

Mandatory qualifiers (bold if not always prompted):

[-algpath] (string)

Location of scop structure-based sequence alignment files (input).

[-algextn] (string)

Extension of alignment files.

-sparsity (integer)

Percentage sparsity of signature.

-seqoption (menu)

Select number.

-datafile (matrixf)

This is the scoring matrix file used when comparing sequences.

-conoption (menu)

Select number.

-filtercon (boolean)

Ignore alignment positions making less than a threshold number of contacts.

-conthresh (integer)

Threshold contact number.

-conpath (string)

Location of contact files (input).

-conextn (string)

Extension of contact files.

-cpdbpath (string)

Location of domain coordinate files (EMBL format input).

-cpdbextn (string)

Extension of coordinate files.

-filterpsim (boolean)

Ignore alignment postitions with post_similar value of 0.

[-sigpath] (string)

Location of signature files (output).

[-sigextn] (string)

Extension of signature files.

Advanced qualifiers:

-randomise (boolean)

Generate a randomized signature.