
                               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
