1 Q9WVI4 : 2 Q9ERL9 : 90.48 1 Q9WVI4 : 3 Q9DGG6 : 55.70 1 Q9WVI4 : 4 Q99396 : 54.74 1 Q9WVI4 : 5 Q99280 : 57.66 2 Q9ERL9 : 3 Q9DGG6 : 58.28 2 Q9ERL9 : 4 Q99396 : 56.39 2 Q9ERL9 : 5 Q99280 : 62.31 3 Q9DGG6 : 4 Q99396 : 52.26 3 Q9DGG6 : 5 Q99280 : 53.99 4 Q99396 : 5 Q99280 : 83.41 |
1 O58452 : 2 O30129 : 82.42 1 O58452 : 3 O26938 : 75.56 2 O30129 : 3 O26938 : 71.43 |
// /ebi/services/idata/pmr/hgmp/test/data/structure/allversusall/swtiny1.fasta // /ebi/services/idata/pmr/hgmp/test/data/structure/allversusall/swtiny2.fasta |
Standard (Mandatory) qualifiers: [-seqinpath] dirlist This option specifies the location of sequence files (input) [-datoutdir] outdir This option specifies the location of sequence similarity data files (output). -logfile outfile This option specifies the name of ALLVERSUSALL log file (output). The log file contains messages about any errors arising while ALLVERSUSALL ran. Additional (Optional) qualifiers: -matrix matrixf This option specifies the residue substitution matrix that is used for sequence comparison. -gapopen float This option specifies the gap insertion penalty. 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. -gapextend float This option specifies the gap extension penalty. 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: "-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 | |
---|---|---|---|
[-seqinpath] (Parameter 1) |
This option specifies the location of sequence files (input) | Directory with files | ./ |
[-datoutdir] (Parameter 2) |
This option specifies the location of sequence similarity data files (output). | Output directory | ./ |
-logfile | This option specifies the name of ALLVERSUSALL log file (output). The log file contains messages about any errors arising while ALLVERSUSALL ran. | Output file | ALLVERSUSALL.log |
Additional (Optional) qualifiers | Allowed values | Default | |
-matrix | This option specifies the residue substitution matrix that is used for sequence comparison. | Comparison matrix file in EMBOSS data path | EBLOSUM62 |
-gapopen | This option specifies the gap insertion penalty. 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 |
-gapextend | This option specifies the gap extension penalty. 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) |
% allversusall Does an all-versus-all global alignment for each set of sequences in an input directory and writes files of sequence similarity values Location of sequence files (input [./]: allversusall/ Location of sequence similarity data files (output) [./]: Name allversusall log file (output) [ALLVERSUSALL.log]: Processing /ebi/services/idata/pmr/hgmp/test/data/structure/allversusall/swtiny1.fasta Processing /ebi/services/idata/pmr/hgmp/test/data/structure/allversusall/swtiny2.fasta |
Go to the output files for this example
Files of sequence sets were read from test_data/allversusall/in and files of sequence similarity values were written to test_data/allversusall/. The log file test_data/allversusall/ALLVERSUSALL.log was written. The file path and extension of the input and output files was specified in the ACD file. The default gap insertion, extension and residue substitution matrix were used.
FILE TYPE | FORMAT | DESCRIPTION | CREATED BY | SEE ALSO |
Domain hits file | DHF format (FASTA-like). | Database hits (sequences) with domain classification information. The hits are relatives to a SCOP or CATH family (or other node in the structural hierarchies) and are found from a search of a discriminating element (e.g. a protein signature, hidden Markov model, simple frequency matrix, Gribskov profile or Hennikoff profile) against a sequence database. | SEQSEARCH (hits retrieved by PSIBLAST). SIGSCAN (hits retrieved by sparse protein signature). LIBSCAN (hits retrieved by various types of HMM and profile). | N.A. |
Program name | Description |
---|---|
aaindexextract | Extract data from AAINDEX |
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) |
ssematch | Searches a DCF file (domain classification file) for secondary structure matches |
tfextract | Extract data from TRANSFAC |