
                              EMBOSS: recoder
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                                Program recoder
                                       
Function

   Remove restriction sites but maintain the same translation
   
Description

   recoder scans a given nucleotide sequence for restriction sites. It
   reports single base positions in the restriction pattern which when
   mutated remove the restriction site whilst maintaining the same
   translation (in frame 1 of the input sequence).
   
   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'.
   
Usage

   Here is a sample session with recoder:

% 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]:

Command line arguments

   Mandatory qualifiers:
  [-seq]               sequence   Nucleic acid sequence
   -enzymes            string     Comma separated enzyme list
  [-outf]              outfile    Results file name

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

   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) 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
   
Input file format

   Normal nucleic acid USA.
   
Output file format

   This is the out[ut from the above example:
     _________________________________________________________________
   
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
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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
   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.
   
Author(s)

   This application was written by Tim Carver (tcarver@hgmp.mrc.ac.uk)
   
History

   Written (January 2001) - Tim Carver
   
   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/
   
Target users

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