recoder

Function

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

Command line arguments


Input file format

recoder reads a normal nucleic acid sequence USA.

Output file format

Data files

Notes

None.

References

None.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with status 0.

Known bugs

None.

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)

History

Target users

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