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recoder |
Several restriction enzymes can be specified or alternatively all the enzymes in the REBASE database can be investigated. To find out whether the single point mutations found by 'recoder', introduce new restriction sites, 'silent' should be run on the original sequence. ('Silent' searches for silent point mutation sites which maintain the same translation.
The output for 'recoder' is similar to the format used by 'silent'.
% recoder Find and remove restriction sites but maintain the same translation Input sequence: em:hsfau Comma separated enzyme list [all]: EcoRII Output file [hsfau.recoder]:
Mandatory qualifiers: [-seq] sequence Nucleic acid sequence -enzymes string Comma separated enzyme list [-outf] outfile Results file name Optional qualifiers: (none) Advanced qualifiers: -sshow boolean Display untranslated sequence -tshow boolean Display translated sequence 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 | |
---|---|---|---|
[-seq] (Parameter 1) |
Nucleic acid sequence | Readable sequence | Required |
-enzymes | Comma separated enzyme list | Any string is accepted | all |
[-outf] (Parameter 2) |
Results file name | Output file | <sequence>.recoder |
Optional qualifiers | Allowed values | Default | |
(none) | |||
Advanced qualifiers | Allowed values | Default | |
-sshow | Display untranslated sequence | Yes/No | No |
-tshow | Display translated sequence | Yes/No | No |
Results for HSFAU: KEY: Enzyme Enzyme name RS-Pattern Restriction enzyme recognition site pattern Match-Posn Position of the first base of RS pattern in sequence AA Amino acid. Original sequence(.)After mutation Base-Posn Position of base to be mutated in sequence Mutation The base mutation to perform Creating silent mutations Enzyme RS-Pattern Match-Posn AA Base-Posn Mutation EcoRII CCWGG 77 P.P 78 C->G EcoRII CCWGG 77 P.P 78 C->A EcoRII CCWGG 77 P.P 78 C->T EcoRII CCWGG 77 R.R 79 A->C EcoRII CCWGG 77 R.R 81 G->A EcoRII CCWGG 107 A.A 108 C->G EcoRII CCWGG 107 A.A 108 C->A EcoRII CCWGG 107 A.A 108 C->T EcoRII CCWGG 107 R.R 109 A->C EcoRII CCWGG 107 R.R 111 G->A EcoRII CCWGG 182 S.S 183 C->G EcoRII CCWGG 182 S.S 183 C->A EcoRII CCWGG 182 S.S 183 C->T EcoRII CCWGG 197 P.P 198 C->G EcoRII CCWGG 197 P.P 198 C->A EcoRII CCWGG 197 P.P 198 C->T EcoRII CCWGG 248 P.P 249 C->G EcoRII CCWGG 248 P.P 249 C->A EcoRII CCWGG 248 P.P 249 C->T EcoRII CCWGG 293 P.P 294 C->G EcoRII CCWGG 293 P.P 294 C->A EcoRII CCWGG 293 P.P 294 C->T Results for reverse of HSFAU: Creating silent mutations Enzyme RS-Pattern Match-Posn AA Base-Posn Mutation EcoRII CCWGG 77 P.P 79 T->G EcoRII CCWGG 77 P.P 79 T->C EcoRII CCWGG 107 P.P 109 T->G EcoRII CCWGG 107 P.P 109 T->C EcoRII CCWGG 182 P.P 184 A->G EcoRII CCWGG 182 P.P 184 A->C EcoRII CCWGG 197 P.P 199 A->G EcoRII CCWGG 197 P.P 199 A->C EcoRII CCWGG 248 P.P 250 A->G EcoRII CCWGG 248 P.P 250 A->C EcoRII CCWGG 293 P.P 295 A->C EcoRII CCWGG 293 P.P 295 A->G
Program name | Description |
---|---|
redata | Search REBASE for enzyme name, references, suppliers etc |
remap | Display a sequence with restriction cut sites, translation etc |
restover | Finds restriction enzymes that produce a specific overhang |
restrict | Finds restriction enzyme cleavage sites |
showseq | Display a sequence with features, translation etc |
silent | Silent mutation restriction enzyme scan |
silent does the opposite to recoder. silent finds sites where a restriction enzyme site can be introduced without changing the translation in frame 1 of the sequence. recoder finds sites where a restriction enzyme site can be removed without changing the translation in frame 1 of the sequence.
Renamed from recode to recoder 16 May 2001 as the old name
clashed with a common UNIX print utility:
http://www.iro.umontreal.ca/contrib/recode/HTML/