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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
Input files for usage example
File: ../domainseqs-keep/all_s.scop
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
DS SEQUENCE 52 AA; 5817 MW; D8CCAE0E1FC0849A CRC64;
ADIEGFTSLA SQCTAQELVM TLNELFARFD KLAAENHCLR IKILGDCYYC VS
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
DS SEQUENCE 65 AA; 7395 MW; 75FBE75B22FD3678 CRC64;
MKFAHLADIH LGYEQFHKPQ REEEFAEAFK NALEIAVQEN VDFILIAGDL FHSSRPSPGT
LKKAI
XX
NC 1
XX
CN [1]
XX
CH A CHAIN; . START; . END;
//
2.0 INPUTS & OUTPUTS
DOMAINNR reads a DCF file (domain classification file) containing
domain sequence information and writes a DCF file in which the
redundant domains are removed from each node (e.g. family, superfamily
etc). Optionally, the redundant domains are written to a second DCF
output file. The node of operation and input and output files are
specified by the user. A log file is also written.
3.0 INPUT FILE FORMAT
The format of the DCF file is described in the SCOPPARSE documentation.
Input files for usage example
File: ../domainseqs-keep/all_s.scop
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
DS SEQUENCE 52 AA; 5817 MW; D8CCAE0E1FC0849A CRC64;
ADIEGFTSLA SQCTAQELVM TLNELFARFD KLAAENHCLR IKILGDCYYC VS
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
DS SEQUENCE 65 AA; 7395 MW; 75FBE75B22FD3678 CRC64;
MKFAHLADIH LGYEQFHKPQ REEEFAEAFK NALEIAVQEN VDFILIAGDL FHSSRPSPGT
LKKAI
XX
NC 1
XX
CN [1]
XX
CH A CHAIN; . START; . END;
//
4.0 OUTPUT FILE FORMAT
The format of the DCF file is described in the SCOPPARSE documentation.
Output files for usage example
File: all_nr.scop
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
DS SEQUENCE 65 AA; 7395 MW; 75FBE75B22FD3678 CRC64;
MKFAHLADIH LGYEQFHKPQ REEEFAEAFK NALEIAVQEN VDFILIAGDL FHSSRPSPGT
LKKAI
XX
NC 1
XX
CN [1]
XX
CH A CHAIN; . START; . END;
//
File: domainnr.log
Classes are non-redundant
5% redundancy threshold
// Alpha and beta proteins (a+b)
Retained
D1II7A_
Rejected
D1CS4A_
5.0 DATA FILES
DOMAINNR requires a residue substitution matrix.
6.0 USAGE
6.1 COMMAND LINE ARGUMENTS
Remove redundant domains from a DCF file.
Version: EMBOSS:6.6.0.0
Standard (Mandatory) qualifiers (* if not always prompted):
[-dcfinfile] infile This option specifies name of 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.
-retain toggle [N] This option specifies whether to write
redundant domains to a separate file. If
this option is selected, redundant domains
are written to a separate output file.
-node menu [1] This option specifies the node for
redundancy removal. Redundancy can be
removed at any specified node in the SCOP or
CATH hierarchies. For example by selecting
'Class' entries belonging to the same Class
will be non-redundant. (Values: 1 (Class
(SCOP)); 2 (Fold (SCOP)); 3 (Superfamily
(SCOP)); 4 (Family (SCOP)); 5 (Class
(CATH)); 6 (Architecture (CATH)); 7
(Topology (CATH)); 8 (Homologous Superfamily
(CATH)); 9 (Family (CATH)))
-mode menu [1] This option specifies whether to remove
redundancy at a single threshold % sequence
similarity or remove redundancy outside a
range of acceptable threshold % similarity.
All permutations of pair-wise sequence
alignments are calculated for each domain
family in turn using the EMBOSS
implementation of the Needleman and Wunsch
global alignment algorithm. Redundant
sequences are removed in one of two modes as
follows: (i) If a pair of proteins achieve
greater than a threshold percentage sequence
similarity (specified by the user) the
shortest sequence is discarded. (ii) If a
pair of proteins have a percentage sequence
similarity that lies outside an acceptable
range (specified by the user) the shortest
sequence is discarded. (Values: 1 (Remove
redundancy at a single threshold % sequence
similarity); 2 (Remove redundancy outside a
range of acceptable threshold % similarity))
* -threshold float [95.0] This option specifies the % sequence
identity redundancy threshold, which
determines the redundancy calculation. If a
pair of proteins achieve greater than this
threshold the shortest sequence is
discarded. (Any numeric value)
* -threshlow float [30.0] This option specifies the % sequence
identity redundancy threshold, which
determines the redundancy calculation. If a
pair of proteins have a percentage sequence
similarity that lies outside an acceptable
range the shortest sequence is discarded.
(Any numeric value)
* -threshup float [90.0] This option specifies the % sequence
identity redundancy threshold, which
determines the redundancy calculation. If a
pair of proteins have a percentage sequence
similarity that lies outside an acceptable
range the shortest sequence is discarded.
(Any numeric value)
[-dcfoutfile] outfile [test.scop] This option specifies the name
of non-redundant DCF file (domain
classification file) (output). 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.
* -redoutfile outfile [*.domainnr] This option specifies the name
of DCF file (domain classification file) for
redundant sequences (output). 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.
-logfile outfile [domainnr.log] This option specifies the
name of log file for the build. The log file
contains messages about any errors arising
while domainnr ran.
Additional (Optional) qualifiers:
-datafile matrixf [EBLOSUM62] This option specifies the
residue substitution matrix. This is used
for sequence comparison.
-gapopen float [10.0 for any sequence] This option
specifies the gap insertion penalty. This 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. This 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. (Floating point number
from 0.0 to 10.0)
Advanced (Unprompted) qualifiers: (none)
Associated qualifiers:
"-dcfoutfile" associated qualifiers
-odirectory2 string Output directory
"-redoutfile" associated qualifiers
-odirectory string Output directory
"-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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