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 nameDescription
recoderRemove restriction sites but maintain the same translation
redataSearch REBASE for enzyme name, references, suppliers etc
remapDisplay a sequence with restriction cut sites, translation etc
restoverFinds restriction enzymes that produce a specific overhang
restrictFinds restriction enzyme cleavage sites
showseqDisplay 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.

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