|   | SSEMATCH documentation | 
| 
SE   HEEE
SS   SEQUENCE    43 AA;   5411 MW;  61C5458D CRC32;
     LLLLLLHHHH EEEEEEEEEE EEEEEEEEEE EELLLEEEEE LLL
 | 
| 
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;
//
 | 
| 
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;
//
 | 
| 
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;
//
 | 
|  | 
| 
    H   E   C   *
H   2 -15  -4  -7
E -15   4  -4  -7
C  -4  -4   2  -7
*  -7  -7  -7   1
 | 
Search a DCF file for secondary structure matches.
Version: EMBOSS:6.6.0.0
   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 | 
| % 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
| 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. | 
| 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 |