Team:NYMU-Taipei/Project/Phosphate/PRIMER of ppk

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biobrick cutting sites scanning report

 * there is a EcoRI cutting site (GAATTC) from 268-273 bp (if 'a' of atg is 1)

>EG11510 ppk 2621066..2623132 E. coli atgGGTCAGG AAAAGCTATA CA TCGAAAAA GAGCTCAGTT GGTTATCGTT CAATGAACGC GTGCTTCAGG AAGCGGCGGA CAAATCTAAC CCGCTGATTG AAAGGATGCG TTTCCTGGGG ATCTATTCCA ATAACCTTGA TGAGTTCTAT AAAGTCCGCT TCGCTGAACT GAAGCGACGC ATCATTATTA GCGAAGAACA AGGCTCCAAC TCTCATTCCC GCCATTTACT GGGCAAAATT CAGTCCCGGG TGCTGAAAGC C GATCAG GAA TTC GACGGC C TCTACAACGA GCTATTGCTG GAGATGGCGC GCAACCAGAT CTTCCTGATT AATGAACGCC AGCTCTCCGT CAATCAACAA AACTGGCTGC GTCATTATTT TAAGCAGTAT CTGCGTCAGC ACATTACGCC GATTTTAATC AATCCTGACA CTGACTTAGT GCAGTTCCTG AAAGATGATT ACACCTATCT GGCGGTGGAA ATTATCCGTG GCGATACCAT CCGTTACGCG CTGCTGGAGA TCCCATCAGA TAAAGTGCCG CGCTTTGTGA ATTTACCGCC AGAAGCGCCG CGTCGACGCA AGCCGATGAT TCTTCTGGAT AACATTCTGC GTTACTGCCT TGATGATATT TTCAAAGGCT TCTTTGATTA TGACGCGCTG AATGCCTATT CAATGAAGAT GACCCGCGAT GCCGAATACG ATTTAGTGCA TGAGATGGAA GCCAGCCTGA TGGAGTTGAT GTCTTCCAGT CTCAAGCAGC GTTTAACTGC TGAGCCGGTG CGTTTTGTTT ATCAGCGCGA TATGCCCAAT GCGCTGGTTG AAGTGTTACG CGAAAAACTG ACTATTTCCC GCTACGACTC CATCGTCCCC GGCGGTCGTT ATCATAATTT TAAAGACTTT ATTAATTTCC CCAATGTCGG CAAAGCCAAT CTGGTGAACA AACCACTGCC GCGTTTACGC CATATTTGGT TTGATAAAGC CCAGTTCCGC AATGGTTTTG ATGCCATTCG CGAACGCGAT GTGTTGCTCT ATTATCCTTA TCACACCTTT GAGCATGTGC TGGAACTGCT GCGTCAGGCT TCGTTCGACC CGAGCGTACT GGCGATTAAA ATTAACATTT ACCGCGTGGC GAAAGATTCA CGCATCATCG ACTCGATGAT CCACGCCGCA CATAACGGTA AGAAAGTCAC CGTGGTGGTT GAGTTACAGG CGCGTTTCGA CGAAGAAGCC AACATTCACT GGGCGAAGCG CCTGACCGAA GCAGGCGTGC ACGTTATCTT CTCTGCGCCG GGGCTGAAAA TTCACGCCAA ACTGTTCCTG ATTTCACGTA AAGAAAACGG TGAAGTGGTG CGTTATGCAC ACATCGGGAC CGGGAACTTT AACGAAAAAA CCGCGCGTCT TTATACTGAC TATTCGTTGC TGACCGCCGA TGCGCGCATC ACCAACGAAG TACGGCGGGT ATTTAACTTT ATTGAAAACC CATACCGTCC GGTGACATTT GATTATTTAA TGGTATCGCC GCAAAACTCC CGCCGCCTAT TGTATGAAAT GGTGGACCGC GAGATCGCCA ACGCGCAGCA AGGGCTGCCC AGTGGTATCA CCCTGAAGCT AAATAACCTT GTCGATAAAG GCCTGGTTGA TCGTCTGTAT GCGGCCTCCA GCTCCGGCGT ACCGGTTAAT CTGCTGGTTC GCGGAATGTG TTCGCTGATC CCCAATCTGG AAGGCATTAG CGACAACATT CGTGCCATCA GTATTGTTGA CCGTTACCTT GAACATGACC GGGTTTATAT TTTTGAAAAT GGCGGCGATA AAAAGGTCTA CCTTTCTTCC GCCGACTGGA TGACGCGCAA TATTGATTAT CGTATTGAAG TGGCGACGCC GCTGCTCGAT CCGCGCCTGA AGCAGCGGGT ACTGGACATC ATCGACATAT TGTTCAGCGA TACGGTCAAA GCACGTTATA TCGATAAAGA ACTCAGTAAT CGCTACGTTC CCCGCGGCAA TCGCCGCAAA GTACGGGCGC AGTTGGCGAT TTATGACTAC AT CAAATCAC TCGAACAACC TGAATAA

mutation

 * to avoid undesired EcoRI cutting site
 * GAA TTC (268-273) at +1 reading frame; it only affects 2 amino acids
 * GAA TTC will be translated into EF (glu, phe)
 * to keep amino acids content, there are several way to mutate
 * glu: GAA → GAG
 * phe: TTC → TTT

biobrick cutting sites scanning report

 * EcoRI cutting site is eliminated
 * No new cutting site is produced

Tools

 * codon table
 * three and one letter code of amino acid