EMBOSS: siggen

Program siggen

Function

Description

Each position in the alignment is scored on the basis of a single or any combination of up to 3 scoring schemes. A signature of, for example, 10% sparsity would include data from the top 10% highest scoring alignment positions.

The resulting protein signature file is used by the application sigscan to find examples of the signature in other proteins.

Signatures

Usage

% 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]:

Command line arguments

   Mandatory qualifiers (* if not always prompted):
  [-algpath]           string     Location of alignment files for input
  [-algextn]           string     Extension of alignment files for input
  [-sparsity]          integer    % sparsity of signature
  [-randomise]         bool       Generate a randomised signature
*  -seqoption          menu       Select number
*  -datafile           matrixf    Substitution matrix to be used
*  -conoption          menu       Select number
*  -filtercon          bool       Ignore alignment positions making less than
                                  a threshold number of contacts
*  -conthresh          integer    Threshold contact number
*  -conpath            string     Location of contact files for input
*  -conextn            string     Extension of contact files
*  -cpdbpath           string     Location of coordinate files for input
                                  (embl-like format)
*  -cpdbextn           string     Extension of coordinate files (embl-like
                                  format)
*  -filterpsim         bool       Ignore alignment postitions with
                                  post_similar value of 0
  [-sigpath]           string     Location of signature files for output
  [-sigextn]           string     Extension of signature files for output

   Optional qualifiers: (none)
   Advanced qualifiers: (none)
   General qualifiers:
  -help                bool       report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose

Mandatory qualifiers		Allowed values	Default
[-algpath] (Parameter 1)	Location of alignment files for input	Any string is accepted	./
[-algextn] (Parameter 2)	Extension of alignment files for input	Any string is accepted	.align
[-sparsity] (Parameter 3)	% sparsity of signature	Any integer value	10
[-randomise] (Parameter 4)	Generate a randomised signature	Yes/No	No
-seqoption	Select number	1 (Substitution matrix) 2 (Residue class) 3 (None)	3
-datafile	Substitution matrix to be used	Comparison matrix file in EMBOSS data path	./EBLOSUM62
-conoption	Select number	1 (Number) 2 (Conservation) 3 (Number and conservation) 4 (None)	4
-filtercon	Ignore alignment positions making less than a threshold number of contacts	Yes/No	No
-conthresh	Threshold contact number	Any integer value	10
-conpath	Location of contact files for input	Any string is accepted	/data/contacts/
-conextn	Extension of contact files	Any string is accepted	.con
-cpdbpath	Location of coordinate files for input (embl-like format)	Any string is accepted	/data/cpdbscop/
-cpdbextn	Extension of coordinate files (embl-like format)	Any string is accepted	.pxyz
-filterpsim	Ignore alignment postitions with post_similar value of 0	Yes/No	No
[-sigpath] (Parameter 5)	Location of signature files for output	Any string is accepted	./
[-sigextn] (Parameter 6)	Extension of signature files for output	Any string is accepted	.sig
Optional qualifiers		Allowed values	Default
(none)
Advanced qualifiers		Allowed values	Default
(none)

Input file format

Output file format

1. CL - Domain class. It is identical to the text given after 'Class' in the scop classification file (see documentation for the EMBOSS application scope).
2. FO - Domain fold. It is identical to the text given after 'Fold' in the scop classification file (see scope documentation).
3. SF - Domain superfamily. It is identical to the text given after 'Superfamily' in the scop classification file (see scope documentation).
4. FA - Domain family. It is identical to the text given after 'Family' in the scop classification file (see scope documentation).
5. NP - Number of signature positions.
6. NN - Signature position number. The number given in brackets after this record indicates the start of the data for the relevent signature positi on.
7. IN - Informative line about signature position. The number of different amino acid residues seen for this position 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 position (see sigscan.c) Two rows of data for the emprical residues and gaps are then given:
8. AA - The identifier of a residue seen in this position and the frequency of its occurence are delimited by ';'.
9. GA - The size of a gap seen in this position and the frequency of its occurence are delimited by ';'.
10. // - used to delimit data for each signature. The last line of a file always contains '//' only.

Example excerpt from an output signature file:

CL   All beta proteins
XX
FO   Lipocalins
XX
SF   Lipocalins
XX
FA   Fatty acid binding protein-like
XX
NP   2
XX
NN   [1] 
XX
IN   NRES 3 ; NGAP 2 ; WSIZ 2  
XX
AA   A ; 2
AA   V ; 1
AA   L ; 4
XX
GA   1 ; 5
GA   2 ; 2
XX
NN   [2] 
XX
IN   NRES 2 ; NGAP 2 ; WSIZ 5  
XX
AA   F ; 1
AA   Y ; 5
XX
GA   12 ; 3
GA   10 ; 2
XX
//

Important

1. In the case a signature file is generated by hand, it is essential that the gap data given is listed in order of increasing gap size.
2. In the current implementation, window size records always have the value of 0. These should be changed manually unless a very rigid pattern is required. 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).
3. Siggen presumes that standard SCOP domain identifiers are given in the input alignment if the id is 7 characters long and the first character is a 'd' or 'D'. In this case the contact data for that chain will be parsed. Otherwise contact data for chain 1 will be parsed.

Data files

EMBOSS data files are distributed with the application and stored in the standard EMBOSS data directory, which is defined by the EMBOSS environment variable EMBOSS_DATA.

To see the available EMBOSS data files, run:

% embossdata -showall

To fetch one of the data files (for example 'Exxx.dat') into your current directory for you to inspect or modify, run:

% embossdata -fetch -file Exxx.dat

Users can provide their own data files in their own directories. Project specific files can be put in the current directory, or for tidier directory listings in a subdirectory called ".embossdata". Files for all EMBOSS runs can be put in the user's home directory, or again in a subdirectory called ".embossdata".

The directories are searched in the following order:

• . (your current directory)
• .embossdata (under your current directory)
• ~/ (your home directory)
• ~/.embossdata

Notes

References

Warnings

Diagnostic Error Messages

Exit status

Known bugs

See also

Author(s)

History

Target users

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