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EMBOSS: seqnr |
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)
% seqnr
Mandatory qualifiers: [-path] string Directory of redundant database search results [-extn] string File extension of redundant database search results files [-outpath] string Directory for proccessed results [-outextn] string File extension for proccessed results files [-datafile] matrixf Residue substitution matrix [-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. [-thresh] float The % sequence identity redundancy threshold Optional qualifiers: (none) Advanced qualifiers: (none) General qualifiers: -help bool report command line options. More information on associated and general qualifiers can be found with -help -verbose |
Mandatory qualifiers | Allowed values | Default | |
---|---|---|---|
[-path] (Parameter 1) |
Directory of redundant database search results | Any string is accepted | ./ |
[-extn] (Parameter 2) |
File extension of redundant database search results files | Any string is accepted | .psiblasts |
[-outpath] (Parameter 3) |
Directory for proccessed results | Any string is accepted | ./ |
[-outextn] (Parameter 4) |
File extension for proccessed results files | Any string is accepted | .clean |
[-datafile] (Parameter 5) |
Residue substitution matrix | Comparison matrix file in EMBOSS data path | EBLOSUM62 |
[-gapopen] (Parameter 6) |
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] (Parameter 7) |
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 |
[-thresh] (Parameter 8) |
The % sequence identity redundancy threshold | Any integer value | 95.0 |
Optional qualifiers | Allowed values | Default | |
(none) | |||
Advanced qualifiers | Allowed values | Default | |
(none) |
Program name | Description |
---|---|
cutgextract | Extract data from CUTG |
domainer | Build domain coordinate files |
nrscope | Converts redundant EMBL-format SCOP file to non-redundant one |
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 | Reads raw-, and writes EMBL-like, scop classification files |
tfextract | Extract data from TRANSFAC |