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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:6.2.0
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:
"-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 | ||||
| "-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 & 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/