EMBOSS: recode


Program recode

Function

Remove restriction sites but maintain the same translation

Description

recode 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 'recode', 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 'recode' is similar to the format used by 'silent'.

Usage

Here is a sample session with recode:

% recode
Find and remove restriction sites but maintain the same translation
Input sequence: em:hsfau
Comma separated enzyme list [all]: EcoRII
Output file [hsfau.recode]:

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


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>.recode
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  


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
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
silentSilent mutation restriction enzyme scan

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 Tim Carver (tcarver@hgmp.mrc.ac.uk)

History

Written (January 2001) - Tim Carver

Target users

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

Comments