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silent |
silent finds positions in a sequence where a point mutation could be made to introduce a specified restriction enzyme recognition site without changing the translation.
Several restriction enzyme can be specified.
% silent Silent mutation restriction enzyme scan Input sequence: embl:hsfau Comma separated enzyme list [all]: ecori,hindiii Output file [hsfau.silent]:
Mandatory qualifiers: [-seq] sequence Sequence USA -enzymes string Comma separated enzyme list [-outf] outfile Output file name Optional qualifiers: (none) Advanced qualifiers: -sshow boolean Display untranslated sequence -tshow boolean Display translated sequence -allmut boolean Display all mutations 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) |
Sequence USA | Readable sequence | Required |
-enzymes | Comma separated enzyme list | Any string is accepted | all |
[-outf] (Parameter 2) |
Output file name | Output file | <sequence>.silent |
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 |
-allmut | Display all mutations | 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 Silent mutations Enzyme RS-Pattern Match-Posn AA Base-Posn Mutation Results for reverse of HSFAU: Silent mutations Enzyme RS-Pattern Match-Posn AA Base-Posn Mutation HindIII AAGCTT 267 A.A 268 A->T
Program name | Description |
---|---|
recoder | Remove restriction sites but maintain the same translation |
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 does the opposite to recode. silent finds sites where a restriction enzyme site can be introduced without changing the translation in frame 1 of the sequence. recode finds sites where a restriction enzyme site can be removed without changing the translation in frame 1 of the sequence.