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SSEMATCH documentation |
SE HEEE
SS SEQUENCE 43 AA; 5411 MW; 61C5458D CRC32;
LLLLLLHHHH EEEEEEEEEE EEEEEEEEEE EELLLEEEEE LLL
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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
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OS Dog (Canis familiaris)
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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
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DO Mre11
XX
OS Archaeon Pyrococcus furiosus
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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;
//
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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;
//
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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;
//
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H E C *
H 2 -15 -4 -7
E -15 4 -4 -7
C -4 -4 2 -7
* -7 -7 -7 1
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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. 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
| 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 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) |
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 | 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 |
| -rgapopen | 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 | 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 | 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 | 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) | |||
% 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 | Generates DCF file from raw CATH files |
| cutgextract | Extract codon usage tables from from CUTG database |
| 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 |
| jaspextract | Extract data from JASPAR |
| 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 database for use by pscan |
| prosextract | Processes the PROSITE motif database for use by patmatmotifs |
| rebaseextract | Process the REBASE database for use by restriction enzyme applications |
| scopparse | Generate DCF file from raw SCOP files |
| seqnr | Removes redundancy from DHF files |
| sites | Generate residue-ligand CON files from CCF files |
| tfextract | Process TRANSFAC transcription factor database for use by tfscan |