| ## EMBOSS: silent

# Program silent

## Function

Silent mutation restriction enzyme scan

## Description

silent does a scan of a nucleic acid sequence for silent mutation restriction enzyme sites.

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.

## Usage

Here is a sample session with silent:

    % silent
    Silent mutation restriction enzyme scan
    Input sequence: embl:hsfau
    Comma separated enzyme list [all]: ecori,hindiii
    Output file [hsfau.silent]:

## Command line arguments

       Mandatory qualifiers:
      [-seq]               sequence   Sequence USA
       -enzymes            string     Comma separated enzyme list
      [-outf]              outfile    Output file name

       Optional qualifiers: (none)
       Advanced qualifiers:
       -sshow              bool       Display untranslated sequence
       -tshow              bool       Display translated sequence
       -allmut             bool       Display all mutations

       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
--- | --- | ---
[-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

## Input file format

Nucleic acid sequence USA.

## Output file format

This is the result of the example above:

    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

## Data files

None.

## Notes

None.

## References

None.

## Warnings

None.

## Diagnostic Error Messages

None.

## Exit status

It always exits with status 0.

## Known bugs

None.

## See also

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.

## Author(s)

This application was written by Alan Bleasby (ableasby@hgmp.mrc.ac.uk)

## History

Written (Aug 2000) - Alan Bleasby.

## Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

## Comments