EMBASSY: SSEMATCH documentation.

SSEMATCH documentation

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

Search a DCF file for secondary structure matches

2.0 INPUTS & OUTPUTS

Reads a DCF file (domain classification file) and a file of secondary structure (query) and writes DCF files containing the top-scoring matches (domains) between the query and domains from the DCF file. The secondary strructure file contains a (1) secondary structure element map (a string where each character represents a secondary structure element) and (2) a secondary structure string (each character represents an amino acid residue) for a given query. Matches are found by global alignment of (1) element maps and (2) strings (individual residues) to generate the two DCF (output) files.
The DCF input file must contain domain secondary structure information, which can be added by using DOMAINSSE.
The names of the secondary structure file, DCF files (input and output) and number of top-scoring matches to report are specified by the user. A log file is also written.

3.0 INPUT FILE FORMAT

Domain classification file
The format of the DCF file is described in the SCOPPARSE documentation.
The DCF input file must contain domain secondary structure information, which can be added by using DOMAINSSE.

Secondary structure file
The format of the secondary structure file (Figure 1) is identical to the SS and SE records from a DCF file (see DOMAINSSE documentation.).
The records are as follows:

(1) SS - Secondary structure assignment (per residue). A simplified 3-state assignment: H (helix), E (extended, beta strand) and L (loop, open coil) should be used.
(2) SE - Secondary structure element assignment (per secondary structure element). The same 3-state assignment as for the SS record should be used.

Note that if the file contains secondary structure characters other than H, E and L they will be converted before they are used by SSEMATCH (see NOTES below).

Input files for usage example

File: sse.in

SE   HEEE
SS   SEQUENCE    43 AA;   5411 MW;  61C5458D CRC32;
     LLLLLLHHHH EEEEEEEEEE EEEEEEEEEE EELLLEEEEE LLL

File: ../domainsse-keep/domainsse.out

ID   D1CS4A_
XX
EN   1CS4
XX
TY   SCOP
XX
SI   53931 CL; 54861 FO; 55073 SF; 55074 FA; 55077 DO; 55078 SO; 39418 DD;
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
DO   Adenylyl cyclase VC1, domain C1a
XX
OS   Dog (Canis familiaris)
XX
SE   HH
XX
SS   SEQUENCE    46 AA;   6039 MW;  32D7FC5C51294C12 CRC64;
     LLLHHHHHHH LLHHHHHHHH HHHHHHHHHH HHHHHLLEEE EEELLL
XX
NC   1
XX
CN   [1]
XX
CH   A CHAIN; . START; . END;
//
ID   D1II7A_
XX
EN   1II7
XX
TY   SCOP
XX
SI   53931 CL; 56299 FO; 56300 SF; 64427 FA; 64428 DO; 64429 SO; 62415 DD;
XX
CL   Alpha and beta proteins (a+b)
XX
FO   Metallo-dependent phosphatases
XX
SF   Metallo-dependent phosphatases
XX
FA   DNA double-strand break repair nuclease
XX
DO   Mre11
XX
OS   Archaeon Pyrococcus furiosus
XX
SE   HEEE
XX
SS   SEQUENCE    43 AA;   5411 MW;  F2A5FA03304F5F35 CRC64;
     LLLLLLHHHH EEEEEEEEEE EEEEEEEEEE EELLLEEEEE LLL
XX
NC   1
XX
CN   [1]
XX
CH   A CHAIN; . START; . END;
//

4.0 OUTPUT FILE FORMAT

The format of the DCF file is described in the SCOPPARSE documentation. SSEMATCH adds an extra comment line at the top containing the score for the appropriate alignment (residue or element).

Output files for usage example

File: res.dcf

XX   ALIGNMENT SCORE 100.000
XX
ID   D1II7A_
XX
EN   1II7
XX
TY   SCOP
XX
SI   53931 CL; 56299 FO; 56300 SF; 64427 FA; 64428 DO; 64429 SO; 62415 DD;
XX
CL   Alpha and beta proteins (a+b)
XX
FO   Metallo-dependent phosphatases
XX
SF   Metallo-dependent phosphatases
XX
FA   DNA double-strand break repair nuclease
XX
DO   Mre11
XX
OS   Archaeon Pyrococcus furiosus
XX
SE   HEEE
XX
SS   SEQUENCE    43 AA;   5411 MW;  F2A5FA03304F5F35 CRC64;
     LLLLLLHHHH EEEEEEEEEE EEEEEEEEEE EELLLEEEEE LLL
XX
NC   1
XX
CN   [1]
XX
CH   A CHAIN; . START; . END;
//

File: elm.dcf

XX   ALIGNMENT SCORE 100.000
XX
ID   D1CS4A_
XX
EN   1CS4
XX
TY   SCOP
XX
SI   53931 CL; 54861 FO; 55073 SF; 55074 FA; 55077 DO; 55078 SO; 39418 DD;
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
DO   Adenylyl cyclase VC1, domain C1a
XX
OS   Dog (Canis familiaris)
XX
SE   HH
XX
SS   SEQUENCE    46 AA;   6039 MW;  32D7FC5C51294C12 CRC64;
     LLLHHHHHHH LLHHHHHHHH HHHHHHHHHH HHHHHLLEEE EEELLL
XX
NC   1
XX
CN   [1]
XX
CH   A CHAIN; . START; . END;
//

File: ssematch.log

5.0 DATA FILES

SSEMATCH requires a secondary structure substitution table such as SSSUB distributed with EMBOSS. An example (taken from Wallqvist et al) is shown in Figure 3.

Figure 3 Excerpt from a DCF (output) file

    H   E   C   *
H   2 -15  -4  -7
E -15   4  -4  -7
C  -4  -4   2  -7
*  -7  -7  -7   1

6.0 USAGE

6.1 COMMAND LINE ARGUMENTS

Search a DCF file for secondary structure matches.
Version: EMBOSS:6.5.0.0

   Standard (Mandatory) qualifiers:
  [-ssinfile]          infile     This option specifies the name of the file
                                  of secondary structure (input).
  [-dcfinfile]         infile     This option specifies the name of the DCF
                                  file (domain classification file) (input). A
                                  'domain classification file' contains
                                  classification and other data for domains
                                  from SCOP or CATH, in DCF format
                                  (EMBL-like). The files are generated by
                                  using SCOPPARSE and CATHPARSE. Domain
                                  sequence information can be added to the
                                  file by using DOMAINSEQS.
   -maxhits            integer    [5] This option specifies the number of
                                  top-scoring matches to report. (Any integer
                                  value)
  [-outssfile]         outfile    [*.ssematch] This option specifies the name
                                  of the file containing top-scoring domains
                                  for residue-based alignment (output).A
                                  'domain classification file' contains
                                  classification and other data for domains
                                  from SCOP or CATH, in DCF format
                                  (EMBL-like).
  [-outsefile]         outfile    [*.ssematch] This option specifies the name
                                  of the file containing top-scoring domains
                                  for secondary structure element-based
                                  alignment (output). A 'domain classification
                                  file' contains classification and other
                                  data for domains from SCOP or CATH, in DCF
                                  format (EMBL-like).
   -logfile            outfile    [ssematch.log] This option specifies the
                                  name of the ssematch log file (output).

   Additional (Optional) qualifiers:
   -datafile           matrixf    [SSSUB] This option specifies the secondary
                                  structure substitution matrix.
   -rgapopen           float      [10.0 for any sequence] This options
                                  specifies the gap insertion penalty for
                                  reside-based alignment. The gap insertion
                                  penalty is the score taken away when a gap
                                  is created. The best value depends on the
                                  choice of comparison matrix. The default
                                  value assumes you are using the EBLOSUM62
                                  matrix for protein sequences, and the
                                  EDNAFULL matrix for nucleotide sequences.
                                  (Floating point number from 1.0 to 100.0)
   -rgapextend         float      [0.5 for any sequence] This options
                                  specifies the gap extension penalty for
                                  residue-based alignment. The gap extension,
                                  penalty is added to the standard gap penalty
                                  for each base or residue in the gap. This
                                  is how long gaps are penalized. Usually you
                                  will expect a few long gaps rather than many
                                  short gaps, so the gap extension penalty
                                  should be lower than the gap penalty.
                                  (Floating point number from 0.0 to 10.0)
   -egapopen           float      [10.0 for any sequence] This options
                                  specifies the gap insertion penalty for
                                  element-based alignment. The gap insertion
                                  penalty is the score taken away when a gap
                                  is created. The best value depends on the
                                  choice of comparison matrix. The default
                                  value assumes you are using the EBLOSUM62
                                  matrix for protein sequences, and the
                                  EDNAFULL matrix for nucleotide sequences.
                                  (Floating point number from 1.0 to 100.0)
   -egapextend         float      [0.5 for any sequence] This options
                                  specifies the gap extension penalty for
                                  secondary structure element-based alignment.
                                  The gap extension, penalty is added to the
                                  standard gap penalty for each base or
                                  residue in the gap. This is how long gaps
                                  are penalized. Usually you will expect a few
                                  long gaps rather than many short gaps, so
                                  the gap extension penalty should be lower
                                  than the gap penalty. (Floating point number
                                  from 0.0 to 10.0)

   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:

   "-outssfile" associated qualifiers
   -odirectory3        string     Output directory

   "-outsefile" associated qualifiers
   -odirectory4        string     Output directory

   "-logfile" associated qualifiers
   -odirectory         string     Output directory

   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

[-ssinfile]
(Parameter 1) infile This option specifies the name of the file of secondary structure (input). Input file Required

[-dcfinfile]
(Parameter 2) infile This option specifies the name of the DCF file (domain classification file) (input). A 'domain classification file' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL-like). The files are generated by using SCOPPARSE and CATHPARSE. Domain sequence information can be added to the file by using DOMAINSEQS. Input file Required

-maxhits integer This option specifies the number of top-scoring matches to report. Any integer value 5

[-outssfile]
(Parameter 3) outfile This option specifies the name of the file containing top-scoring domains for residue-based alignment (output).A 'domain classification file' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL-like). Output file <*>.ssematch

[-outsefile]
(Parameter 4) outfile This option specifies the name of the file containing top-scoring domains for secondary structure element-based alignment (output). A 'domain classification file' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL-like). Output file <*>.ssematch

-logfile outfile This option specifies the name of the ssematch log file (output). Output file ssematch.log

Additional (Optional) qualifiers

-datafile matrixf This option specifies the secondary structure substitution matrix. Comparison matrix file in EMBOSS data path SSSUB

-rgapopen float This options specifies the gap insertion penalty for reside-based alignment. The gap insertion penalty is the score taken away when a gap is created. The best value depends on the choice of comparison matrix. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide sequences. Floating point number from 1.0 to 100.0 10.0 for any sequence

-rgapextend float This options specifies the gap extension penalty for residue-based alignment. The gap extension, penalty is added to the standard gap penalty for each base or residue in the gap. This is how long gaps are penalized. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty. Floating point number from 0.0 to 10.0 0.5 for any sequence

-egapopen float This options specifies the gap insertion penalty for element-based alignment. The gap insertion penalty is the score taken away when a gap is created. The best value depends on the choice of comparison matrix. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide sequences. Floating point number from 1.0 to 100.0 10.0 for any sequence

-egapextend float This options specifies the gap extension penalty for secondary structure element-based alignment. The gap extension, penalty is added to the standard gap penalty for each base or residue in the gap. This is how long gaps are penalized. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty. Floating point number from 0.0 to 10.0 0.5 for any sequence

Advanced (Unprompted) qualifiers

(none)

Associated qualifiers

"-outssfile" associated outfile qualifiers

-odirectory3
-odirectory_outssfile string Output directory Any string

"-outsefile" associated outfile qualifiers

-odirectory4
-odirectory_outsefile string Output directory Any string

"-logfile" associated outfile qualifiers

-odirectory string Output directory Any string

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

Qualifier	Type	Description	Allowed values	Default
Standard (Mandatory) qualifiers
[-ssinfile] (Parameter 1)	infile	This option specifies the name of the file of secondary structure (input).	Input file	Required
[-dcfinfile] (Parameter 2)	infile	This option specifies the name of the DCF file (domain classification file) (input). A 'domain classification file' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL-like). The files are generated by using SCOPPARSE and CATHPARSE. Domain sequence information can be added to the file by using DOMAINSEQS.	Input file	Required
-maxhits	integer	This option specifies the number of top-scoring matches to report.	Any integer value	5
[-outssfile] (Parameter 3)	outfile	This option specifies the name of the file containing top-scoring domains for residue-based alignment (output).A 'domain classification file' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL-like).	Output file	<>*.ssematch
[-outsefile] (Parameter 4)	outfile	This option specifies the name of the file containing top-scoring domains for secondary structure element-based alignment (output). A 'domain classification file' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL-like).	Output file	<>*.ssematch
-logfile	outfile	This option specifies the name of the ssematch log file (output).	Output file	ssematch.log
Additional (Optional) qualifiers
-datafile	matrixf	This option specifies the secondary structure substitution matrix.	Comparison matrix file in EMBOSS data path	SSSUB
-rgapopen	float	This options specifies the gap insertion penalty for reside-based alignment. The gap insertion penalty is the score taken away when a gap is created. The best value depends on the choice of comparison matrix. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide sequences.	Floating point number from 1.0 to 100.0	10.0 for any sequence
-rgapextend	float	This options specifies the gap extension penalty for residue-based alignment. The gap extension, penalty is added to the standard gap penalty for each base or residue in the gap. This is how long gaps are penalized. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty.	Floating point number from 0.0 to 10.0	0.5 for any sequence
-egapopen	float	This options specifies the gap insertion penalty for element-based alignment. The gap insertion penalty is the score taken away when a gap is created. The best value depends on the choice of comparison matrix. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide sequences.	Floating point number from 1.0 to 100.0	10.0 for any sequence
-egapextend	float	This options specifies the gap extension penalty for secondary structure element-based alignment. The gap extension, penalty is added to the standard gap penalty for each base or residue in the gap. This is how long gaps are penalized. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty.	Floating point number from 0.0 to 10.0	0.5 for any sequence
Advanced (Unprompted) qualifiers
(none)
Associated qualifiers
"-outssfile" associated outfile qualifiers
-odirectory3 -odirectory_outssfile	string	Output directory	Any string
"-outsefile" associated outfile qualifiers
-odirectory4 -odirectory_outsefile	string	Output directory	Any string
"-logfile" associated outfile qualifiers
-odirectory	string	Output directory	Any string
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

An example of interactive use of SSEMATCH is shown below. Here is a sample session with ssematch

% ssematch Search a DCF file for secondary structure matches. Secondary structure file: sse.in Domain classification file: ../domainsse-keep/domainsse.out Number of top-scoring matches to report. [5]: 1 Domain classification residue-based output file [sse.ssematch]: res.dcf Domain classification structure-based output file [sse.out2]: elm.dcf Domainatrix log output file [ssematch.log]:

Go to the input files for this example
Go to the output files for this example

7.0 KNOWN BUGS & WARNINGS

The SSEMATCH implementation of secondary structure mapping is the most basic and more powerful algorithms are available. Input file
The DCF input file must contain domain secondary structure information, which can be added by using DOMAINSSE.

8.0 NOTES

Conversion of secondary structure file
SSEMATCH currently only works with 3-state secondary structure assignments. The following conversions are applied to the characters in the secondary structure input file:

Bridge B/b, turn T, coil C are changed to 'L'.
Helices 'H', 'G', 'I' are changed to / remain 'H'.
Extended conformation ('E') remains 'E'.

8.1 GLOSSARY OF FILE TYPES

FILE TYPE	FORMAT	DESCRIPTION	CREATED BY	SEE ALSO
Domain classification file (for SCOP)	DCF format (EMBL-like).	Classification and other data for domains from SCOP.	SCOPPARSE	Domain sequence information can be added to the file by using DOMAINSEQS.
Domain classification file (for CATH)	DCF format (EMBL-like).	Classification and other data for domains from CATH.	CATHPARSE	Domain sequence information can be added to the file by using DOMAINSEQS.

None

9.0 DESCRIPTION

Secondary structure element mapping is a coarse but powerful approach for identifying similarities between protein sequences. SSEMATCH implements a very basic approach whereby a query sequence of secondary structure (of elements or residues) is scanned against a library of known secondary structures for domains in SCOP or CATH, as held in a DCF file (domain classification file).

10.0 ALGORITHM

Standard N&W-type global alignment.

11.0 RELATED APPLICATIONS

Program name	Description
aaindexextract	Extract amino acid property data from AAINDEX
allversusall	Sequence similarity data from all-versus-all comparison
cathparse	Generate DCF file from raw CATH files
cutgextract	Extract codon usage tables from CUTG database
domainalign	Generate alignments (DAF file) for nodes in a DCF file
domainer	Generate domain CCF files from protein CCF files
domainnr	Remove redundant domains from a DCF file
domainrep	Reorder DCF file to identify representative structures
domainseqs	Add sequence records to a DCF file
domainsse	Add secondary structure records to a DCF file
helixturnhelix	Identify nucleic acid-binding motifs in protein sequences
hetparse	Convert heterogen group dictionary to EMBL-like format
jaspextract	Extract data from JASPAR
libgen	Generate discriminating elements from alignments
matgen3d	Generate a 3D-1D scoring matrix from CCF files
pdbparse	Parse PDB files and writes protein CCF files
pdbplus	Add accessibility and secondary structure to a CCF file
pdbtosp	Convert swissprot:PDB codes file to EMBL-like format
pepcoil	Predict coiled coil regions in protein sequences
printsextract	Extract data from PRINTS database for use by pscan
prosextract	Process the PROSITE motif database for use by patmatmotifs
rebaseextract	Process the REBASE database for use by restriction enzyme applications
rocon	Generate a hits file from comparing two DHF files
rocplot	Perform ROC analysis on hits files
scopparse	Generate DCF file from raw SCOP files
seqalign	Extend alignments (DAF file) with sequences (DHF file)
seqfraggle	Remove fragment sequences from DHF files
seqnr	Remove redundancy from DHF files
seqsort	Remove ambiguous classified sequences from DHF files
seqwords	Generate DHF files from keyword search of UniProt
sites	Generate residue-ligand CON files from CCF files
tfextract	Process TRANSFAC transcription factor database for use by tfscan

12.0 DIAGNOSTIC ERROR MESSAGES

None.

13.0 AUTHORS

Amanda O'Reilly
Jon Ison (jison@ebi.ac.uk)
The European Bioinformatics Institute Wellcome Trust Genome Campus Cambridge CB10 1SD UK

14.0 REFERENCES

Please cite the authors and EMBOSS.

Rice P, Bleasby A.J. 2000. EMBOSS - The European Molecular Biology Open Software Suite. Trends in Genetics, 15:276-278. See also http://www.uk.embnet.org/Software/EMBOSS

14.1 Other useful references

Wallqvist A, Fukunishi Y, Murphy LR, Fadel A, Levy RM.
Iterative sequence/secondary structure search for protein homologs: comparison with amino acid sequence alignments and application to fold recognition in genome databases.
Bioinformatics. 2000 Nov;16(11):988-1002.