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scopnr |
This package is still being developed.
Please ignore this program until further details can be documented.
All further queries should go to Jon Ison. (Jon Ison)
% scopnr
Mandatory qualifiers (* if not always prompted): [-scopin] infile Name of scop classification file (embl format input) -mode menu Select number * -thresh float The % sequence identity redundancy threshold * -threshlow float The % sequence identity redundancy threshold (lower limit) * -threshup float The % sequence identity redundancy threshold (upper limit) [-scopout] outfile Name of non-redundant scop classification file (embl format output) -errf outfile Name of log file for the build Optional qualifiers: -datafile matrixf This is the scoring matrix file used when comparing sequences. -gapopen float 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. -gapextend float 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. Advanced qualifiers: (none) General qualifiers: -help boolean Report command line options. More information on associated and general qualifiers can be found with -help -verbose |
Mandatory qualifiers | Allowed values | Default | |||||
---|---|---|---|---|---|---|---|
[-scopin] (Parameter 1) |
Name of scop classification file (embl format input) | Input file | Escop.dat | ||||
-mode | Select number |
|
1 | ||||
-thresh | The % sequence identity redundancy threshold | Any numeric value | 95.0 | ||||
-threshlow | The % sequence identity redundancy threshold (lower limit) | Any numeric value | 30.0 | ||||
-threshup | The % sequence identity redundancy threshold (upper limit) | Any numeric value | 90.0 | ||||
[-scopout] (Parameter 2) |
Name of non-redundant scop classification file (embl format output) | Output file | Escop_90.dat | ||||
-errf | Name of log file for the build | Output file | scopnr.log | ||||
Optional qualifiers | Allowed values | Default | |||||
-datafile | This is the scoring matrix file used when comparing sequences. | Comparison matrix file in EMBOSS data path | EBLOSUM62 | ||||
-gapopen | 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 | 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 qualifiers | Allowed values | Default | |||||
(none) |
Program name | Description |
---|---|
aaindexextract | Extract data from AAINDEX |
cutgextract | Extract data from CUTG |
domainer | Reads protein coordinate files and writes domains coordinate files |
funky | Reads clean coordinate files and writes file of protein-heterogen contact data |
groups | Removes redundant hits from a scop families file |
hetparse | Converts raw dictionary of heterogen groups to a file in embl-like format |
nrscope | Converts redundant EMBL-format SCOP file to non-redundant one |
pdbparse | Parses pdb files and writes cleaned-up protein coordinate files |
pdbtosp | Convert raw swissprot:pdb equivalence file to embl-like format |
printsextract | Extract data from PRINTS |
prosextract | Builds the PROSITE motif database for patmatmotifs to search |
rebaseextract | Extract data from REBASE |
scope | Convert raw scop classification file to embl-like format |
scopparse | Converts raw scop classification files to a file in embl-like format |
scopseqs | Adds pdb and swissprot sequence records to a scop classification file |
tfextract | Extract data from TRANSFAC |