recoder finds restriction enzyme sites in a nucleotide sequence which can be removed without changing the translation. recoder scans a nucleotide sequence for restriction sites for a supplied set of restriction enzymes. It writes a standard EMBOSS report of single base positions which, when mutated, remove the restriction site whilst maintaining the same translation in frame 1 of the input sequence. One or more restriction enzymes can be specified or alternatively all the enzymes in the REBASE database can be investigated. Optionally, the untranslated and translated sequence may be reported.
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To find out whether the single point mutations found by recoder introduce new restriction sites, silent should be run on the original sequence. 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 uses the EMBOSS REBASE restriction enzyme data files stored in directory data/REBASE/* under the EMBOSS installation directory. These files must first be set up using the program rebaseextract. Running rebaseextract may be the job of your system manager.
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.