EMBOSS: recoder

| ## EMBOSS: recoder

# 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

## 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