New Restriction Sites In Silent Mutations

This program scans a reading frame for new digest sites that can be created by silent mutations. It uses the conventional codon codes. The input sequence is always considered as linear, that is, a specified reading frame can not span over the ends (this limitation may be removed in the future), and the reading frame must be on the top strand (you must know how to get around if the reading frame of your interest happens to be on the bottom strand). The program uses rebase (derived from rebase of NAR format from the ftp site vent.neb.com) as the source of restriction enzymes.

In the output, the sequences of the new restriction sites, tagged with the names of their corresponding enzymes, are aligned with the sequence (but not wrapped if spanning over ends of sequence lines). The mutations needed are shown in upper cases. The translated amino acid sequence and their codon families are also aligned under the sequence. Note that it is critical to display or print the result with a fixed-width font in order to view the result properly.

You can scan a reading frame with a set of specified enzymes (a enzyme name must be given in the standard way with NO space(s) in it) or with all (commercially available) enzymes in the database (but only one enzyme is shown in the result if there are more than one isoschizomer; you can run another program on this site to list isoschizomers or enzymes that recognize the same sequence).

Several options are available for users to set some requirements such as types of cutting ends, cutting length, the number of mutations needed to create a new site. 

Example:

	342 bps, ORF: 100-201

Requirements:
	Commercially vailable
	Cutting length: 6
	Mutations allowed: 1-2

M: A or C    R: A or G    W: A or T    S: C or G    Y: C or T    K: G or T
V: not T     H: not G     D: not C     B: not A     N: any

                                                               agTact-ScaI
                                                           gataTC-EcoRV
                                                          tgatCa-BclI
                                                     GatnnnnatC-Bsh1365I
                                                    cGatCg-PvuI
                             GgtCtc-Eco31I          caatTg-MunI
                             CgtCtc-Esp3I           cTryag-BfmI
                           ctCgtg-Bst2BI            cGryCg-Bsh1285I
      AACAGCGAAGGGTATTATTTCCTTGTGTCAGATAAGATGCTATATGCAATAGTGATAAGC
       .80       .90       .100      .110      .120      .130  
                           LeuValSerAspLysMetLeuTyrAlaIleValIleSer
                           TTRGTNTCNGAYAARATGTTRTAYGCNATHGTNATHTCN
                           CTN   AGY         CTN               AGY

                                            catTgc-BsrDI
                                  cGatCg-PvuI
                                  cAattg-MunI
                                  ctryAg-BfmI   gcAttC-BsmI
                       ttcGaa-NspV    CgannnnnnTgc-BcgI
              GdgChc-Bsp1286I     cGryCg-Bsh1285I
      ACTATTCTATGTCCATATTCAAAATATGCTATTGAATACATAGCTTTTAACTTCATAAAG
       .140      .150      .160      .170      .180      .190  
      ThrIleLeuCysProTyrSerLysTyrAlaIleGluTyrIleAlaPheAsnPheIleLys
      ACNATHTTRTGYCCNTAYTCNAARTAYGCNATHGARTAYATHGCNTTYAAYTTYATHAAR
            CTN         AGY                                       

      AAAGATTTTTTCGAAAGAAGAAAAAACCTAAATAACGCCCCCGTAGCAAAATTAAACCTA
       .200      .210      .220      .230      .240      .250  
      Lys                                                         
      AAR
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