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;  C2EA3A0F CRC32;
     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;  61C5458D CRC32;
     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;  61C5458D CRC32;
     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;  C2EA3A0F CRC32;
     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

   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    This option specifies the number of
                                  top-scoring matches to report.
  [-outssfile]         outfile    This option specifies the name of the file
                                  containing top-scoring domains for
                                  residue-based alinnment (output).A 'domain
                                  classification file' contains classification
                                  and other data for domains from SCOP or
                                  CATH, in DCF format (EMBL-like).
  [-outsefile]         outfile    This option specifies the name of the file
                                  containing top-scoring domains for secondary
                                  structure element-based alinnment (output).
                                  A 'domain classification file' contains
                                  classification and other data for domains
                                  from SCOP or CATH, in DCF format
                                  (EMBL-like).
   -logfile            outfile    This option specifies the name of the
                                  ssematch log file (output).

   Additional (Optional) qualifiers:
   -datafile           matrixf    This option specifies the secondary
                                  structure substitution matrix.
   -gapopenr           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.
   -gapextendr         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.
   -gapopene           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.
   -gapextende         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.

   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 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 deaths

Standard (Mandatory) qualifiers Allowed values Default

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

[-dcfinfile]
(Parameter 2) 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 This option specifies the number of top-scoring matches to report. Any integer value 5

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

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

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

Additional (Optional) qualifiers Allowed values Default

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

-gapopenr 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

-gapextendr 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

-gapopene 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

-gapextende 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 Allowed values Default

(none)

Standard (Mandatory) qualifiers	Allowed values	Default
[-ssinfile] (Parameter 1)	This option specifies the name of the file of secondary structure (input).	Input file	Required
[-dcfinfile] (Parameter 2)	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	This option specifies the number of top-scoring matches to report.	Any integer value	5
[-outssfile] (Parameter 3)	This option specifies the name of the file containing top-scoring domains for residue-based alinnment (output).A 'domain classification file' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL-like).	Output file	<sequence>.ssematch
[-outsefile] (Parameter 4)	This option specifies the name of the file containing top-scoring domains for secondary structure element-based alinnment (output). A 'domain classification file' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL-like).	Output file
-logfile	This option specifies the name of the ssematch log file (output).	Output file	ssematch.log
Additional (Optional) qualifiers	Allowed values	Default
-datafile	This option specifies the secondary structure substitution matrix.	Comparison matrix file in EMBOSS data path	SSSUB
-gapopenr	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
-gapextendr	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
-gapopene	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
-gapextende	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	Allowed values	Default
(none)

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. Name of file of secondary structure (input).: sse.in Name of DCF file (domain classification file) (input).: ../domainsse-keep/domainsse.out Number of top-scoring matches to report. [5]: 1 Name of DCF file (domain classification file) containing top-scoring domains for residue-based alinnment (output). [sse.ssematch]: res.dcf Name of DCF file (domain classification file) containing top-scoring domains for secondary structure element-based alinnment (output). [sse.out2]: elm.dcf Name ssematch log file (output) [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 data from AAINDEX
allversusall	Sequence similarity data from all-versus-all comparison
cathparse	Generates DCF file from raw CATH files
cutgextract	Extract data from CUTG
domainer	Generates domain CCF files from protein CCF files
domainnr	Removes redundant domains from a DCF file
domainseqs	Adds sequence records to a DCF file
domainsse	Add secondary structure records to a DCF file
hetparse	Converts heterogen group dictionary to EMBL-like format
pdbparse	Parses PDB files and writes protein CCF files
pdbplus	Add accessibility & secondary structure to a CCF file
pdbtosp	Convert swissprot:PDB codes file to EMBL-like format
printsextract	Extract data from PRINTS
prosextract	Build the PROSITE motif database for use by patmatmotifs
rebaseextract	Extract data from REBASE
scopparse	Generate DCF file from raw SCOP files
seqnr	Removes redundancy from DHF files
sites	Generate residue-ligand CON files from CCF files
tfextract	Extract data from TRANSFAC

12.0 DIAGNOSTIC ERROR MESSAGES

None.

13.0 AUTHORS

Amanda O'Reilly (aoreilly@rfcgr.mrc.ac.uk)
Jon Ison (jison@rfcgr.mrc.ac.uk)
MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, 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.