
SSEMATCH 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

   Searches a DCF file (domain classification 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: all_e.scop

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   EEEEEEE
XX
SS   SEQUENCE   189 AA;  24290 MW;  D1929097 CRC32;
     LLLLLLLEEE EEEEEEEEEE ELHHHHHHHL LHHHHHHHHH HHHHHHHHHH HHHHLLEEEE
     EELLEEEEEE LLLLLLLHHH HHHHHHHHHH HHHHHHHHHH HHLLLLEEEE EEEEEEEEEL
     LLLLLLLLEE EHHHHHHHHH HHHHLLLLLE EEEHHHHHLL LLLLLEEELH HHHHHHHHHH
     HLLLEEEEL
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   EEEEEEE
XX
SS   SEQUENCE   189 AA;  24290 MW;  D1929097 CRC32;
     LLLLLLLEEE EEEEEEEEEE ELHHHHHHHL LHHHHHHHHH HHHHHHHHHH HHHHLLEEEE
     EELLEEEEEE LLLLLLLHHH HHHHHHHHHH HHHHHHHHHH HHLLLLEEEE EEEEEEEEEL
     LLLLLLLLEE EHHHHHHHHH HHHHLLLLLE EEEHHHHHLL LLLLLEEELH HHHHHHHHHH
     HLLLEEEEL
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. An exception is where one or
                                  both sequences are single reads with
                                  possible sequencing errors in which case you
                                  would expect many single base gaps. You can
                                  get this result by setting the gap open
                                  penalty to zero (or very low) and using the
                                  gap extension penalty to control gap
                                  scoring.
   -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. An
                                  exception is where one or both sequences are
                                  single reads with possible sequencing
                                  errors in which case you would expect many
                                  single base gaps. You can get this result by
                                  setting the gap open penalty to zero (or
                                  very low) and using the gap extension
                                  penalty to control gap scoring.

   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. An exception is where one or both
   sequences are single reads with possible sequencing errors in which
   case you would expect many single base gaps. You can get this result
   by setting the gap open penalty to zero (or very low) and using the
   gap extension penalty to control gap scoring. 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. An exception
   is where one or both sequences are single reads with possible
   sequencing errors in which case you would expect many single base
   gaps. You can get this result by setting the gap open penalty to zero
   (or very low) and using the gap extension penalty to control gap
   scoring. 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 
Searches a DCF file (domain classification file) for secondary structure
matches.
Name of file of secondary structure (input).: sse.in
Name of DCF file (domain classification file) (input).: all_e.scop
Number of top-scoring matches to report. [5]: 1
Name of DCF file (domain classification file) containing top-scoring domains fo
r residue-based alinnment (output). [sse.ssematch]: res.dcf
Name of DCF file (domain classification file) containing top-scoring domains fo
r 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

   Two strings (for residues and elements) of secondary structure were
   read from sse.in and scanned against all_e.scop. The single highest
   scoring match for each search was written to the output files: res.dcf
   for residue-based alignment and elm.dcf for element-based alignment. A
   log file called SSEMATCH.log was written.

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

See also

   Program name Description
   aaindexextract Extract data from AAINDEX
   allversusall Does an all-versus-all global alignment for each set of
   sequences in an input directory and writes files of sequence
   similarity values
   cathparse Reads raw CATH classification files and writes DCF file
   (domain classification file)
   cutgextract Extract data from CUTG
   domainer Reads CCF files (clean coordinate files) for proteins and
   writes CCF files for domains, taken from a DCF file (domain
   classification file)
   domainnr Removes redundant domains from a DCF file (domain
   classification file). The file must contain domain sequence
   information, which can be added by using DOMAINSEQS
   domainseqs Adds sequence records to a DCF file (domain classification
   file)
   domainsse Adds secondary structure records to a DCF file (domain
   classification file)
   hetparse Converts raw dictionary of heterogen groups to a file in
   EMBL-like format
   pdbparse Parses PDB files and writes CCF files (clean coordinate
   files) for proteins
   pdbplus Add residue solvent accessibility and secondary structure data
   to a CCF file (clean coordinate file) for a protein or domain
   pdbtosp Convert raw swissprot:PDB equivalence file to EMBL-like format
   printsextract Extract data from PRINTS
   prosextract Builds the PROSITE motif database for patmatmotifs to
   search
   rebaseextract Extract data from REBASE
   scopparse Reads raw SCOP classification files and writes a DCF file
   (domain classification file)
   seqnr Removes redundancy from DHF files (domain hits files) or other
   files of sequences
   sites Reads CCF files (clean coordinate files) and writes CON files
   (contact files) of residue-ligand contact data for domains in a DCF
   file (domain classification file)
   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.
