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CONTENTS
1.0 SUMMARY
2.0 INPUTS & OUTPUTS
3.0 INPUT FILE FORMAT
4.0 OUTPUT FILE FORMAT
5.0 DATA FILES
6.0 USAGE
7.0 KNOWN BUGS & WARNINGS
8.0 NOTES
9.0 DESCRIPTION
10.0 ALGORITHM
11.0 RELATED APPLICATIONS
12.0 DIAGNOSTIC ERROR MESSAGES
13.0 AUTHORS
14.0 REFERENCES
1.0 SUMMARY
Sequence similarity data from all-versus-all comparison
2.0 INPUTS & OUTPUTS
ALLVERSUSALL reads a directory of files each containing a set of 2 or
more sequences, performs an all-versus-all global alignment on each set
and writes a file of sequence similarity values for each input file.
The output files have the same base name as the input files. The path
and extension of the input and output files are specified by the user
in the ACD file.
3.0 INPUT FILE FORMAT
All common sequence format are supported.
4.0 OUTPUT FILE FORMAT
The output file contains 7 columns as follows:
* (1) Sequence number (sequential order in input file) of first
sequence of a pair.
* (2) Accesion number of first sequence of a pair.
* (3) A ':' is always given.
* (4) Sequence number of second sequence.
* (5) Accesion number of second sequence.
* (6) A ':' is always given.
* (7) Sequence similarity value (2dp).
Output files for usage example
File: swtiny1.out
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
File: swtiny2.out
1 O58452 : 2 O30129 : 82.42
1 O58452 : 3 O26938 : 75.56
2 O30129 : 3 O26938 : 71.43
File: allversusall.log
//
/homes/user/test/data/structure/allversusall/swtiny1.fasta
//
/homes/user/test/data/structure/allversusall/swtiny2.fasta
5.0 DATA FILES
ALLVERSUSALL uses a residue substitution matrix.
6.0 USAGE
6.1 COMMAND LINE ARGUMENTS
Sequence similarity data from all-versus-all comparison.
Version: EMBOSS:6.6.0.0
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
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