SIGGEN documentation

CONTENTS

1.0 SUMMARY

2.0 INPUTS & OUTPUTS

3.0 INPUT FILE FORMAT

4.0 OUTPUT FILE FORMAT

• 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.

• 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

6.0 USAGE

6.1 COMMAND LINE ARGUMENTS

Generates a sparse protein signature from an alignment
Version: EMBOSS:6.3.0

   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:

   "-algpath" associated qualifiers
   -extension1         string     Default file extension

   "-conpath" associated qualifiers
   -extension          string     Default file extension

   "-cpdbpath" associated qualifiers
   -extension          string     Default file extension

   "-sigoutdir" associated qualifiers
   -extension2         string     Default file extension

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to 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 and exit. 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
   -version            boolean    Report version number and exit

Qualifier	Type	Description	Allowed values	Default
Standard (Mandatory) qualifiers
[-algpath] (Parameter 1)	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.	Directory with files	./
-mode	list	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.	1 (Use positions specified in alignment file) 2 (Use a scoring method) 3 (Generate a randomised signature)	1
-conoption	list	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.	1 (Number) 2 (Conservation) 3 (Number and conservation) 4 (None (structural data available)) 5 (None (no structural data available))	5
-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.	Directory	./
-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.	Directory	./
-seqoption	list	This option specifies the sequence-based scoring scheme. SIGGEN provides 2 sequence-based scoring schemes that are used to score the input alignment.	1 (Substitution matrix) 2 (Residue class) 3 (None)	3
-datafile	matrixf	This option specifies the the substitution matrix. The substitution matrix is used by the sequence-based scoring schemes.	Comparison matrix file in EMBOSS data path	EBLOSUM62
-sparsity	integer	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	10
-wsiz	integer	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	0
-filtercon	toggle	This option specifies whether to disregard positions forming few contacts only during the selection of signature positions.	Toggle value Yes/No	No
-conthresh	integer	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	10
-[no]filterpsim	boolean	This option specifies whether to disregard alignment sites that were not aligned satisfactorily (STAMP alignments only).	Boolean value Yes/No	Yes
[-sigoutdir] (Parameter 2)	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.	Output directory	./
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
(none)
Associated qualifiers
"-algpath" associated dirlist qualifiers
-extension1 -extension_algpath	string	Default file extension	Any string	daf
"-conpath" associated directory qualifiers
-extension	string	Default file extension	Any string	con
"-cpdbpath" associated directory qualifiers
-extension	string	Default file extension	Any string	ccf
"-sigoutdir" associated outdir qualifiers
-extension2 -extension_sigoutdir	string	Default file extension	Any string	sig
General qualifiers
-auto	boolean	Turn off prompts	Boolean value Yes/No	N
-stdout	boolean	Write first file to standard output	Boolean value Yes/No	N
-filter	boolean	Read first file from standard input, write first file to standard output	Boolean value Yes/No	N
-options	boolean	Prompt for standard and additional values	Boolean value Yes/No	N
-debug	boolean	Write debug output to program.dbg	Boolean value Yes/No	N
-verbose	boolean	Report some/full command line options	Boolean value Yes/No	Y
-help	boolean	Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose	Boolean value Yes/No	N
-warning	boolean	Report warnings	Boolean value Yes/No	Y
-error	boolean	Report errors	Boolean value Yes/No	Y
-fatal	boolean	Report fatal errors	Boolean value Yes/No	Y
-die	boolean	Report dying program messages	Boolean value Yes/No	Y
-version	boolean	Report version number and exit	Boolean value Yes/No	N

6.2 EXAMPLE SESSION

% siggen Generates a sparse protein signature from an alignment Domain alignment directories [./]: ../domainalign-keep/daf Specify mode of signature generation 1 : Use positions specified in alignment file 2 : Use a scoring method 3 : Generate a randomised signature Select number [1]: 2 Residue contacts scoring method 1 : Number 2 : Conservation 3 : Number and conservation 4 : None (structural data available) 5 : None (no structural data available) Select number [5]: 5 Sequence variability scoring method 1 : Substitution matrix 2 : Residue class 3 : None Select number [3]: 1 Substitution matrix to be used [EBLOSUM62]: EBLOSUM62 The % sparsity of signature [10]: 15 Window size [0]: 0 Ignore alignment positions with post_similar value of 0 [Y]: Y Domainatrix signature file output directory [./]:

Go to the output files for this example

7.0 KNOWN BUGS & WARNINGS

8.0 NOTES

8.1 GLOSSARY OF FILE TYPES

9.0 DESCRIPTION

10.0 ALGORITHM

11.0 RELATED APPLICATIONS

See also

12.0 DIAGNOSTIC ERROR MESSAGES

14.0 REFERENCES

See also http://emboss.sourceforge.net/

Automatic generation and evaluation of sparse protein signatures for families of protein structural domains. MJ Blades, JC Ison, R Ranasinghe, and JBC Findlay. Protein Science. 2005 (accepted)

A key residues approach to the definition of protein families and analysis of sparse family signatures. JC Ison, AJ Bleasby, MJ Blades, SC Daniel, JH Parish, JBC Findlay. PROTEINS: Structure, Function & Genetics. 2000, 40:330-341

Alignment of a sparse protein signature with protein sequences: application to fold prediction for three small globulins. SC Daniel, JH Parish, JC Ison, MJ Blades & JBC Findlay. FEBS Letters. 1999, 459:349-352.

14.1 Other useful references