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scopseqs |
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)
% scopseqs
Mandatory qualifiers: [-scopin] infile Name of scop file for input (embl-like format) [-pdbtosp] infile Name of the pdbcodes to swissprot indexing (embl-like format) [-dpdb] string Location of clean domain coordinate files for input (embl-like format) [-extn] string File extension of clean domain coordinate files [-scopout] outfile Name of processed file for output (embl-like format) [-errf] outfile Name of log file for the build Optional qualifiers: (none) Advanced 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. 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 file for input (embl-like format) | Input file | Escop.dat |
[-pdbtosp] (Parameter 2) |
Name of the pdbcodes to swissprot indexing (embl-like format) | Input file | Epdbtosp.dat |
[-dpdb] (Parameter 3) |
Location of clean domain coordinate files for input (embl-like format) | Any string is accepted | ./ |
[-extn] (Parameter 4) |
File extension of clean domain coordinate files | Any string is accepted | .pxyz |
[-scopout] (Parameter 5) |
Name of processed file for output (embl-like format) | Output file | Escop.dat.out |
[-errf] (Parameter 6) |
Name of log file for the build | Output file | scopseqs.log |
Optional qualifiers | Allowed values | Default | |
(none) | |||
Advanced 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 |
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 |
scopnr | Removes redundant domains from a scop classification file |
scopparse | Converts raw scop classification files to a file in embl-like format |
tfextract | Extract data from TRANSFAC |