|   | ALLVERSUSALL documentation | 
| 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 | 
| // /homes/user/test/data/structure/allversusall/swtiny1.fasta // /homes/user/test/data/structure/allversusall/swtiny2.fasta | 
Sequence similarity data from all-versus-all comparison.
Version: EMBOSS:6.4.0.0
   Standard (Mandatory) qualifiers:
  [-seqinpath]         dirlist    [./] Sequence directories
  [-datoutdir]         outdir     [./] This option specifies the location of
                                  sequence similarity data files (output).
   -logfile            outfile    [allversusall.log] 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    [EBLOSUM62] This option specifies the
                                  residue substitution matrix that is used for
                                  sequence comparison.
   -gapopen            float      [10.0 for any sequence] 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)
   -gapextend          float      [0.5 for any sequence] 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)
   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:
   "-seqinpath" associated qualifiers
   -extension1         string     Default file extension
   "-datoutdir" associated qualifiers
   -extension2         string     Default file extension
   "-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 | ||||
| [-seqinpath] (Parameter 1) | dirlist | Sequence directories | Directory with files | ./ | 
| [-datoutdir] (Parameter 2) | outdir | This option specifies the location of sequence similarity data files (output). | Output directory | ./ | 
| -logfile | outfile | 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 | ||||
| -matrix | matrixf | This option specifies the residue substitution matrix that is used for sequence comparison. | Comparison matrix file in EMBOSS data path | EBLOSUM62 | 
| -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. | Floating point number from 1.0 to 100.0 | 10.0 for any sequence | 
| -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. | Floating point number from 0.0 to 10.0 | 0.5 for any sequence | 
| Advanced (Unprompted) qualifiers | ||||
| (none) | ||||
| Associated qualifiers | ||||
| "-seqinpath" associated dirlist qualifiers | ||||
| -extension1 -extension_seqinpath | string | Default file extension | Any string | fasta | 
| "-datoutdir" associated outdir qualifiers | ||||
| -extension2 -extension_datoutdir | string | Default file extension | Any string | out | 
| "-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 | 
| % allversusall Sequence similarity data from all-versus-all comparison. Sequence directories [./]: allversusall/ Location of sequence similarity data files (output) [./]: Domainatrix log output file [allversusall.log]: Processing /homes/user/test/data/structure/allversusall/swtiny1.fasta Processing /homes/user/test/data/structure/allversusall/swtiny2.fasta | 
Go to the output files for this example
| 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 amino acid property data from AAINDEX | 
| cathparse | Generates DCF file from raw CATH files | 
| cutgextract | Extract codon usage tables 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 and 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 | 
| ssematch | Search a DCF file for secondary structure matches | 
| tfextract | Process TRANSFAC transcription factor database for use by tfscan | 
See also http://emboss.sourceforge.net/