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DOMAINNR documentation |
CONTENTS
1.0 SUMMARY2.0 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;
//
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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;
//
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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
| Qualifier | Type | Description | Allowed values | Default | ||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Standard (Mandatory) qualifiers | ||||||||||||||||||||||
| [-dcfinfile] (Parameter 1) |
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. | Input file | Required | ||||||||||||||||||
| -retain | toggle | 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. | Toggle value Yes/No | No | ||||||||||||||||||
| -node | list | 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. |
|
1 | ||||||||||||||||||
| -mode | list | 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. |
|
1 | ||||||||||||||||||
| -threshold | float | 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 | 95.0 | ||||||||||||||||||
| -threshlow | float | 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 | 30.0 | ||||||||||||||||||
| -threshup | float | 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 | 90.0 | ||||||||||||||||||
| [-dcfoutfile] (Parameter 2) |
outfile | 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. | Output file | test.scop | ||||||||||||||||||
| -redoutfile | outfile | 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. | Output file | <*>.domainnr | ||||||||||||||||||
| -logfile | outfile | This option specifies the name of log file for the build. The log file contains messages about any errors arising while domainnr ran. | Output file | domainnr.log | ||||||||||||||||||
| Additional (Optional) qualifiers | ||||||||||||||||||||||
| -datafile | matrixf | This option specifies the residue substitution matrix. This is used for sequence comparison. | Comparison matrix file in EMBOSS data path | EBLOSUM62 | ||||||||||||||||||
| -gapopen | float | 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 | 10.0 for any sequence | ||||||||||||||||||
| -gapextend | float | 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 | 0.5 for any sequence | ||||||||||||||||||
| Advanced (Unprompted) qualifiers | ||||||||||||||||||||||
| (none) | ||||||||||||||||||||||
| Associated qualifiers | ||||||||||||||||||||||
| "-dcfoutfile" associated outfile qualifiers | ||||||||||||||||||||||
| -odirectory2 -odirectory_dcfoutfile |
string | Output directory | Any string | |||||||||||||||||||
| "-redoutfile" associated outfile qualifiers | ||||||||||||||||||||||
| -odirectory | string | Output directory | Any string | |||||||||||||||||||
| "-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 | ||||||||||||||||||
6.2 EXAMPLE SESSION
An example of interactive use of DOMAINNR is shown below. Here is a sample session with domainnr
% domainnr
Remove redundant domains from a DCF file.
Domain classification file: ../domainseqs-keep/all_s.scop
Write redundant domains to separate file. [N]:
Node at which to remove redundancy
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)
Select number. [1]: 1
Redundancy removal options
1 : Remove redundancy at a single threshold % sequence similarity
2 : Remove redundancy outside a range of acceptable threshold % similarity
Select number. [1]: 1
The % sequence identity redundancy threshold. [95.0]: 5
Domain classification output file [test.scop]: all_nr.scop
Domainatrix log output file [domainnr.log]:
Warning: Bad args passed to ajDomainWrite
// Alpha and beta proteins (a+b)
D1CS4A_
D1II7A_
|
Go to the input files for this example
Go to the output files for this example
7.0 KNOWN BUGS & WARNINGS
None.8.0 NOTES
If for example the user selected the node to be "Family (SCOP)" then DOMAINNR removes redundancy at the level of the SCOP family, i.e. entries belonging to the same family will be non-redundant.8.1 GLOSSARY OF FILE TYPES
| FILE TYPE | FORMAT | DESCRIPTION | CREATED BY | SEE ALSO |
| Domain classification file (for SCOP) | DCF format (EMBL-like format for domain classification data). | Classification and other data for domains from SCOP. | SCOPPARSE | Domain sequence information can be added to the file by using DOMAINSEQS. |
| Domain classification file (for CATH) | DCF format (EMBL-like format for domain classification data). | Classification and other data for domains from CATH. | CATHPARSE | Domain sequence information can be added to the file by using DOMAINSEQS. |
9.0 DESCRIPTION
The inclusion of very similar sequences in certain analyses will introduce undesirable bias. For example, a family may possess 100 sequences in the sequence database, but 90 of these might be essentially the same sequence, e.g. very close relatives or mutations of a single sequence. Although 100 sequences are known, the family only contains 11 sequences that are essentially unique. For many methods it is desirable to use sets of sequences that are truly representative of the larger family. DOMAINNR reads a DCF file (domain classification file) and writes a DCF file with redundant domains removed from each node in the domain classification hierarchy, e.g. family, superfamily or class.10.0 ALGORITHM
All permutations of pair-wise sequence alignments are calculated for each node (family etc) 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. The user must specify gap insertion and extension penalties and a residue substitution matrix for use in the alignments. % sequence similarity is calculated by using the EMBOSS function embAlignCalcSimilarity.11.0 RELATED APPLICATIONS
See also
| Program name | Description |
|---|---|
| aaindexextract | Extract amino acid property data from AAINDEX |
| allversusall | Sequence similarity data from all-versus-all comparison |
| cathparse | Generate DCF file from raw CATH files |
| cutgextract | Extract codon usage tables from CUTG database |
| domainalign | Generate alignments (DAF file) for nodes in a DCF file |
| domainer | Generate domain CCF files from protein CCF files |
| domainrep | Reorder DCF file to identify representative structures |
| domainseqs | Add sequence records to a DCF file |
| domainsse | Add secondary structure records to a DCF file |
| helixturnhelix | Identify nucleic acid-binding motifs in protein sequences |
| hetparse | Convert heterogen group dictionary to EMBL-like format |
| jaspextract | Extract data from JASPAR |
| libgen | Generate discriminating elements from alignments |
| matgen3d | Generate a 3D-1D scoring matrix from CCF files |
| pdbparse | Parse 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 |
| pepcoil | Predict coiled coil regions in protein sequences |
| printsextract | Extract data from PRINTS database for use by pscan |
| prosextract | Process the PROSITE motif database for use by patmatmotifs |
| rebaseextract | Process the REBASE database for use by restriction enzyme applications |
| rocon | Generate a hits file from comparing two DHF files |
| rocplot | Perform ROC analysis on hits files |
| scopparse | Generate DCF file from raw SCOP files |
| seqalign | Extend alignments (DAF file) with sequences (DHF file) |
| seqfraggle | Remove fragment sequences from DHF files |
| seqnr | Remove redundancy from DHF files |
| seqsort | Remove ambiguous classified sequences from DHF files |
| seqwords | Generate DHF files from keyword search of UniProt |
| 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 |
12.0 DIAGNOSTIC ERROR MESSAGES
DOMAINNR generates a log file an excerpt of which is shown in Figure 1. The first two lines give the level in the SCOP or CATH hierarchy at which redundancy was removed (e.g. 'Families') and the value of the redundancy threshold. The file then contains a section for each node, e.g. each family. Each section contains a line with the record '//' immediately followed by the name of the node (family in this case), and two lines containing 'Retained' and 'Rejected' respectively. Domain identifier codes of domains that appear in output file are listed under 'Retained', while redundant domains are listed under 'Rejected'. Tthese will be saved in a second output file if the user has specified redundant domains to be retained. The text 'ERROR filename file read error' will be given when an error was encountered during a file read.Figure 1 Summary of ROCPLOT output
Excerpt from DOMAINNR log file Families are non-redundant 95% redundancy threshold // Homeodomain Retained D2HDDA_ D1AKHA_ D1MNMC_ Rejected D2HDDB_ D1ENH__ D3HDDA_ WARN d3hdda_.pxyz not found // Di-haem cytohrome c peroxidase WARN ds005__.pxyz not found WARN Empty family // Nuclear receptor coactivator Src-1 Retained D2PRGC_ Rejected |
13.0 AUTHORS
Ranjeeva RanasingheJon Ison (jison@ebi.ac.uk)
The European Bioinformatics Institute Wellcome Trust Genome Campus Cambridge CB10 1SD UK
14.0 REFERENCES
Please cite the authors and EMBOSS.Rice P, Longden I and Bleasby A (2000) "EMBOSS - The European Molecular Biology Open Software Suite" Trends in Genetics, 15:276-278.
See also http://emboss.sourceforge.net/