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 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; // |
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; // |
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; // |
|
H E C * H 2 -15 -4 -7 E -15 4 -4 -7 C -4 -4 2 -7 * -7 -7 -7 1 |
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) |
% 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 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
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.
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 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 |