Which site of NDV NP gene is cut by BamHI and XhoI? - (Nov/08/2005 )
Currently, I am using BamHI and XhoI to cut Newcastle Disease Virus nucleocapsid gene,the gene sequence is as followed :
  1 atgtcttccg tattcgatga atacgagcag ctcctcgctg ctcagactcg ccccaatgga
       61 gctcacggag ggggagagag agggagcact ttaagagttg aggtcccagt attcactctt
      121 aacagtgacg atccagaaga tagatggaat tttgcggtat tctgtcttcg gattgctgtt
      181 agcgaggacg ccaacaaacc gctcaggcaa ggtgctctca tatccctcct gtgctcccat
      241 tctcaagtga tgaggaacca tgttgccctt gcaggaaaac agaatgaggc tacactgact
      301 gttcttgaga tcgatggttt taccagcagc gtgcctcagt tcaacaacag gagtggggtg
      361 tctgaggaga gagcacagag attcatggtg atagcagggt ctctccctcg ggcgtgcagt
      421 aacggtactc cgttcgtcac ggctggggtt gaagatgatg caccagaaga tatcactgat
      481 actctggaaa gaatcctgtc tatccaggct caggtatggg tcacagtagc gaaggccatg
      541 actgcatatg agacagcaga tgagtcggaa acaagaagaa tcaataagta catgcagcaa
      601 ggcagagtcc agaagaagta catcctccac cctgtatgca ggagtgcaat tcaactcaca
      661 atcagacatt ctctggcagt ccgcattttc ttagttagcg agcttaagag aggccgcaat
      721 acggcaggtg ggagctccac gtattacaac ttagtagggg atgtagactc atacatcagg
      781 aacaccggac ttactgcatt cttccttaca ctcaaatatg gaattaatac caagacatca
      841 gccctagcac tcagcagcct cacaggcgat atccaaaaga tgaagcagct catgcgttta
      901 tatcggatga agggagaaaa tgcgccgtac atgacattgc taggtgacag tgatcagatg
      961 agctttgcac cggctgagta tgcacagctt tattcttttg ccatgggcat ggcatcagtc
     1021 ttagataaag gaactggcaa ataccaattc gccagagact tcatgagcac atcattctgg
     1081 agactcgggg tggagtatgc tcaggctcag gggagtagca tcaacgaaga catggctgct
     1141 gagctaaaac taaccccggc agcaagaagg ggcctggcag ctgctgccca acgagtgtct
     1201 gaggaaactg gcagcgtgga tattcctact caacaagccg gggtcctcac tgggctcagc
     1261 gatggaggcc cccgagcctc tcagggtgga tcgaacaagt cgcaagggca accagatgcc
     1321 ggagatgggg agacccaatt cttggatttg atgagagcag tggcgaacag catgcgagaa
     1381 gcgccaaact ccgcacagag caccacccac ccggaacccc ccccgactcc cgggccatca
     1441 caagataacg acaccgactg ggggtattga
My lecturer suggested me to use BamHI and XhoI to cut this sequence in order to clone this gene into a plasmid. However, I could not find the restriction site of the enzymes (BamHI and XhoI) that I used in this sequence.
I would be more than happy if anyone could provide a free of charge website for me to locate the restriction site, or help me to locate the restriction site.
Thank you.
These are the sties that I found using a program called DNAStar (not free).  These are all unique sites.
Sequence : seq.seq ( 1 > 1470 )         44 Unique Sites
Enzymes  : All 242 enzymes (No Filter), 127 Enzymes Cut
Settings  : Linear, Certain Sites Only, Standard Genetic Code
  
  715  AarI     
  764  AccI     
  703  AflII    
 1183  AlwNI    
  147  ApoI     
  824  AseI     
  951  BclI     
  863  BglI     
 1098  BpmI     
  740  BsaAI    
  188  BsaHI    
  784  BsaWI    
  442  BseYI    
  435  BsgI     
   88  BsmFI    
  796  BsmI     
 1061  BspHI    
  715  BspMI    
  201  BsrBI    
  934  BsrDI    
  969  BsrFI    
 1008  BstXI    
 1001  BtgI     
 1364  BtsI     
  311  ClaI     
 1098  Eco57MI  
 1384  HaeII    
  196  HgaI     
  765  Hpy8I    
  739  HpyCH4IV 
  545  MmeI     
 1006  MslI     
 1180  MspA1I   
 1001  NcoI     
  546  NdeI     
 1341  PflMI    
 1180  PvuII    
 1431  SmaI     
 1374  SphI     
 1001  StyI     
  716  TauI     
  742  TscI     
  140  XcmI     
 1429  XmaI   
I hope it helps.  
1 atgtcttccg tattcgatga atacgagcag ctcctcgctg ctcagactcg ccccaatgga
61 gctcacggag ggggagagag agggagcact ttaagagttg aggtcccagt attcactctt
121 aacagtgacg atccagaaga tagatggaat tttgcggtat tctgtcttcg gattgctgtt
181 agcgaggacg ccaacaaacc gctcaggcaa ggtgctctca tatccctcct gtgctcccat
241 tctcaagtga tgaggaacca tgttgccctt gcaggaaaac agaatgaggc tacactgact
301 gttcttgaga tcgatggttt taccagcagc gtgcctcagt tcaacaacag gagtggggtg
361 tctgaggaga gagcacagag attcatggtg atagcagggt ctctccctcg ggcgtgcagt
421 aacggtactc cgttcgtcac ggctggggtt gaagatgatg caccagaaga tatcactgat
481 actctggaaa gaatcctgtc tatccaggct caggtatggg tcacagtagc gaaggccatg
541 actgcatatg agacagcaga tgagtcggaa acaagaagaa tcaataagta catgcagcaa
601 ggcagagtcc agaagaagta catcctccac cctgtatgca ggagtgcaat tcaactcaca
661 atcagacatt ctctggcagt ccgcattttc ttagttagcg agcttaagag aggccgcaat
721 acggcaggtg ggagctccac gtattacaac ttagtagggg atgtagactc atacatcagg
781 aacaccggac ttactgcatt cttccttaca ctcaaatatg gaattaatac caagacatca
841 gccctagcac tcagcagcct cacaggcgat atccaaaaga tgaagcagct catgcgttta
901 tatcggatga agggagaaaa tgcgccgtac atgacattgc taggtgacag tgatcagatg
961 agctttgcac cggctgagta tgcacagctt tattcttttg ccatgggcat ggcatcagtc
1021 ttagataaag gaactggcaa ataccaattc gccagagact tcatgagcac atcattctgg
1081 agactcgggg tggagtatgc tcaggctcag gggagtagca tcaacgaaga catggctgct
1141 gagctaaaac taaccccggc agcaagaagg ggcctggcag ctgctgccca acgagtgtct
1201 gaggaaactg gcagcgtgga tattcctact caacaagccg gggtcctcac tgggctcagc
1261 gatggaggcc cccgagcctc tcagggtgga tcgaacaagt cgcaagggca accagatgcc
1321 ggagatgggg agacccaatt cttggatttg atgagagcag tggcgaacag catgcgagaa
1381 gcgccaaact ccgcacagag caccacccac ccggaacccc ccccgactcc cgggccatca
1441 caagataacg acaccgactg ggggtattga
My lecturer suggested me to use BamHI and XhoI to cut this sequence in order to clone this gene into a plasmid. However, I could not find the restriction site of the enzymes (BamHI and XhoI) that I used in this sequence.
I would be more than happy if anyone could provide a free of charge website for me to locate the restriction site, or help me to locate the restriction site.
Thank you.
hi
download pDRAW (http://www.acaclone.com/, download section) and after installation, click on "file" enter new sequence. You'll get your stuff.
