
                           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

   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

   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 alinnment (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
                                  alinnment (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.
   -gapopenr           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)
   -gapextendr         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)
   -gapopene           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)
   -gapextende         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 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 dying program messages

