
                            SIGGEN documentation
                                      
   

CONTENTS

   1.0 SUMMARY 
   2.0 INPUTS & OUTPUTS 
   3.0 INPUT FILE FORMAT 
   4.0 OUTPUT FILE FORMAT 
   5.0 DATA FILES 
   6.0 USAGE 
   7.0 KNOWN BUGS & WARNINGS 
   8.0 NOTES 
   9.0 DESCRIPTION 
   10.0 ALGORITHM 
   11.0 RELATED APPLICATIONS 
   12.0 DIAGNOSTIC ERROR MESSAGES 
   13.0 AUTHORS 
   14.0 REFERENCES 

1.0 SUMMARY

   Generates a sparse protein signature from an alignment

2.0 INPUTS & OUTPUTS

   SIGGEN reads a directory of DAF files (domain alignment files) and,
   optionally, a directory of CON files (contacts file) containing a CON
   file for each aligned domain. It generates a sparse protein signature
   of a specified sparsity for each alignment. The base name of a
   signature file is the unique identifier (an integer) for the family,
   superfamily etc if one is specified in the DAF file, otherwise, the
   base name of the input DAF file is used. The paths of the input and
   output files are specified by the user and the file extensions are
   specified in the ACD file.

3.0 INPUT FILE FORMAT

   The format of the domain alignment file is described in DOMAINALIGN
   documentation.

4.0 OUTPUT FILE FORMAT

   The output file (Figure 1) uses the following records. Domain
   classification records for the node in SCOP or CATH from which the
   input alignment and therefore signature were derived are given. In
   this example, the four records taken from the DAF (input) file are CL,
   FO, SF and FA.
     * TY - Signature type, either SCOP or CATH for domain signatures, or
       LIGAND for ligand signatures.
     * TS - Signature data type, either 1D or 3D, for sequence or
       structure-based signatures respectively.
     * CL - Domain class.
     * FO - Domain fold.
     * SF - Domain superfamily.
     * FA - Domain family.
     * SI - Unique identifier of the node in question, e.g. SCOP Sunid of
       a domain family.
     * NP - Number of signature positions.
     * NN - Signature position number. The number given in brackets
       indicates the start of the data for the relevent signature
       position.
     * IN - Informative line about signature position. The number of
       different observed amino acid residues is given after 'NRES', the
       number of different sizes of gap follows 'NGAP', and the window
       size after 'WSIZ'. When a signature is aligned to a protein
       sequence, the permissible gaps between two signature positions is
       determined by the empirical gaps and the window size for the
       C-terminal most position of the pair.

   Two rows of data for the emprical residues and gaps are then given:
     * AA - The identifier of a residue seen in this position and the
       frequency of its occurence are delimited by ';'.
     * GA - The size of a gap seen in this position and the frequency of
       its occurence are delimited by ';'.
     * // - used to delimit data for each signature. The last line of a
       file always contains '//' only.

  Output files for usage example

  File: 54894.sig

TY   SCOP
XX
TS   1D
XX
CL   Alpha and beta proteins (a+b)
XX
FO   Ferredoxin-like
XX
SF   Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain
XX
FA   Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain
XX
SI   54894
XX
NP   15
XX
NN   [1]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   H ; 2
XX
GA   12 ; 2
XX
NN   [2]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   P ; 2
XX
GA   1 ; 2
XX
NN   [3]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   P ; 2
XX
GA   26 ; 2
XX
NN   [4]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   T ; 2
XX
GA   15 ; 2
XX
NN   [5]
XX


  [Part of this file has been deleted for brevity]

XX
GA   4 ; 2
XX
NN   [10]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   I ; 2
XX
GA   2 ; 2
XX
NN   [11]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   D ; 2
XX
GA   0 ; 2
XX
NN   [12]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   N ; 2
XX
GA   0 ; 2
XX
NN   [13]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   V ; 2
XX
GA   3 ; 2
XX
NN   [14]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   R ; 2
XX
GA   3 ; 2
XX
NN   [15]
XX
IN   NRES 1 ; NGAP 1 ; WSIZ 0
XX
AA   L ; 2
XX
GA   2 ; 2
//

  File: 55074.sig

TY   SCOP
XX
TS   1D
XX
CL   Alpha and beta proteins (a+b)
XX
FO   Ferredoxin-like
XX
SF   Adenylyl and guanylyl cyclase catalytic domain
XX
FA   Adenylyl and guanylyl cyclase catalytic domain
XX
SI   55074
XX
NP   38
XX
NN   [1]
XX
IN   NRES 2 ; NGAP 2 ; WSIZ 0
XX
AA   H ; 1
AA   E ; 1
XX
GA   10 ; 1
GA   11 ; 1
XX
NN   [2]
XX
IN   NRES 2 ; NGAP 1 ; WSIZ 0
XX
AA   D ; 1
AA   T ; 1
XX
GA   1 ; 2
XX
NN   [3]
XX
IN   NRES 2 ; NGAP 1 ; WSIZ 0
XX
AA   I ; 1
AA   T ; 1
XX
GA   3 ; 2
XX
NN   [4]
XX
IN   NRES 2 ; NGAP 1 ; WSIZ 0
XX
AA   F ; 1
AA   I ; 1


  [Part of this file has been deleted for brevity]

AA   N ; 1
XX
GA   4 ; 2
XX
NN   [34]
XX
IN   NRES 2 ; NGAP 2 ; WSIZ 0
XX
AA   K ; 1
AA   A ; 1
XX
GA   4 ; 1
GA   8 ; 1
XX
NN   [35]
XX
IN   NRES 2 ; NGAP 1 ; WSIZ 0
XX
AA   W ; 1
AA   A ; 1
XX
GA   0 ; 2
XX
NN   [36]
XX
IN   NRES 2 ; NGAP 2 ; WSIZ 0
XX
AA   A ; 1
AA   T ; 1
XX
GA   14 ; 1
GA   16 ; 1
XX
NN   [37]
XX
IN   NRES 2 ; NGAP 1 ; WSIZ 0
XX
AA   K ; 1
AA   X ; 1
XX
GA   2 ; 2
XX
NN   [38]
XX
IN   NRES 2 ; NGAP 1 ; WSIZ 0
XX
AA   G ; 1
AA   D ; 1
XX
GA   1 ; 2
//

5.0 DATA FILES

   SIGGEN requires a residue substitution matrix.

6.0 USAGE

  6.1 COMMAND LINE ARGUMENTS

   Standard (Mandatory) qualifiers (* if not always prompted):
  [-algpath]           dirlist    [./] This option specifies the location of
                                  DAF files (domain alignment files) (input).
                                  A 'domain alignment file' contains a
                                  sequence alignment of domains belonging to
                                  the same SCOP or CATH family (or other node
                                  in the structural hierarchies). The file is
                                  in DAF format (CLUSTAL-like) and is
                                  annotated with domain family classification
                                  information. The files generated by using
                                  SCOPALIGN will contain a structure-based
                                  sequence alignment of domains of known
                                  structure only. Such alignments can be
                                  extended with sequence relatives (of unknown
                                  structure) by using SEQALIGN.
   -mode               menu       [1] This option specifies the mode of
                                  signature generation. There are 3 modes for
                                  signatures generatation: (1) Use positions
                                  specified in alignment file. The alignment
                                  file must contain a line beginning with the
                                  text 'Positions' for each line of the
                                  alignment. A '1' in the 'Positions' line
                                  indicates that the signature should include
                                  data from the corresponding alignment site.
                                  The signature will only include the
                                  positions that are marked with a '1'. (2)
                                  Use a scoring method. The alignment is
                                  scored (see 'Algorithm') and the signature
                                  of a specified sparsity is sampled from high
                                  scoring positions. (3): Generate a
                                  randomised signature. A signature of a
                                  specified sparsity is sampled at random from
                                  the alignment. (Values: 1 (Use positions
                                  specified in alignment file); 2 (Use a
                                  scoring method); 3 (Generate a randomised
                                  signature))
*  -conoption          menu       [5] This option specifies the
                                  structure-based scoring scheme. SIGGEN
                                  provides 2 structure-based scoring schemes
                                  (plus a combination method) that are used to
                                  score the input alignment. (Values: 1
                                  (Number); 2 (Conservation); 3 (Number and
                                  conservation); 4 (None (structural data
                                  available)); 5 (None (no structural data
                                  available)))
*  -conpath            directory  [./] This option specifies the location of
                                  CON files (contact files) (input). A
                                  'contact file' contains contact data for a
                                  protein or a domain from SCOP or CATH, in
                                  the CON format (EMBL-like). The contacts may
                                  be intra-chain residue-residue, inter-chain
                                  residue-residue or residue-ligand. The
                                  files are generated by using CONTACTS,
                                  INTERFACE and SITES.
*  -cpdbpath           directory  [./] This option specifies the location of
                                  domain CCF files (clean coordinate files)
                                  (input). A 'clean cordinate file' contains
                                  protein coordinate and derived data for a
                                  single PDB file ('protein clean coordinate
                                  file') or a single domain from SCOP or CATH
                                  ('domain clean coordinate file'), in CCF
                                  format (EMBL-like). The files, generated by
                                  using PDBPARSE (PDB files) or DOMAINER
                                  (domains), contain 'cleaned-up' data that is
                                  self-consistent and error-corrected.
                                  Records for residue solvent accessibility
                                  and secondary structure are added to the
                                  file by using PDBPLUS.
*  -seqoption          menu       [3] This option specifies the sequence-based
                                  scoring scheme. SIGGEN provides 2
                                  sequence-based scoring schemes that are used
                                  to score the input alignment. (Values: 1
                                  (Substitution matrix); 2 (Residue class); 3
                                  (None))
*  -datafile           matrixf    [EBLOSUM62] This option specifies the the
                                  substitution matrix. The substitution matrix
                                  is used by the sequence-based scoring
                                  schemes.
*  -sparsity           integer    [10] This option specifies the % sparsity of
                                  signature. The signature sparsity is a
                                  user-defined parameter that determines how
                                  many residues the final signature will
                                  contain, for example, if the average
                                  sequence length of the proteins in the
                                  alignment is 250 residues, then a signature
                                  of sparsity 10% (default value) will contain
                                  25 key residues or signature positions,
                                  that correspond to the top 25% highest
                                  scoring alignment positions. (Any integer
                                  value)
   -wsiz               integer    [0] This option specifies the window size.
                                  When a signature is aligned to a protein
                                  sequence, the permissible gaps between two
                                  signature positions is determined by the
                                  empirical gaps and the window size. The user
                                  is prompted for a window size that is used
                                  for every position in the signature. Likely
                                  this is not optimal. A future implementation
                                  will provide a range of methods for
                                  generating values of window size depending
                                  upon the alignment (window size is
                                  identified by the WSIZ record in the
                                  signature output file). (Any integer value)
*  -filtercon          toggle     [N] This option specifies whether to
                                  disregard positions forming few contacts
                                  only during the selection of signature
                                  positions.
*  -conthresh          integer    [10] This option specifies the threshold
                                  contact number. This controls the selection
                                  of key positions for the structure-based
                                  scoring scheme (number of contacts). (Any
                                  integer value)
*  -[no]filterpsim     boolean    [Y] This option specifies whether to
                                  disregard alignment sites that were not
                                  aligned satisfactorily (STAMP alignments
                                  only).
  [-sigoutdir]         outdir     [./] This option specifies the location of
                                  signature files (output). A 'signature file'
                                  contains a sparse sequence signature
                                  suitable for use with the SIGSCAN and SIGGEN
                                  programs. The files are generated by using
                                  SIGGEN & SIGGENLIG.

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers: (none)
   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write standard output
   -filter             boolean    Read standard input, write standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages

