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):
Advanced qualifiers:
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