Difference between revisions of "Part:BBa K4790068:Design"

 
 
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===Design Notes===
 
===Design Notes===
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Firstly, we use profile-HMM algorithm instead of BLAST local alignment algorithm. To obtain PETase-related protein sequences from all species, Pfam entries and HMMER web server were used to search Swiss-prot and NCBI public databases. Then we set up a database of PETase protein sequences by selecting relatively strict sequences according to e-value, and manually adding sequences identified by homology. Finally, the phylogenetic tree was established through the ML algorithm of fireprot server, and several ancestor sequences of PETase were obtained according to the evolved nodes, among which the most primitive sequence was node 98.
+
Firstly, we use profile-HMM algorithm instead of BLAST local alignment algorithm. To obtain PETase-related protein sequences from all species, Pfam entries and HMMER web server were used to search Swiss-prot and NCBI public databases. Then we set up a database of PETase protein sequences by selecting relatively strict sequences according to e-value, and manually adding sequences identified by homology. Finally, the phylogenetic tree was established through the ML algorithm of fireprot server, and several ancestor sequences of PETase were obtained according to the evolved nodes, among which the most primitive sequence was node 100.
  
  

Latest revision as of 01:27, 29 September 2023


ASR3(node 100)


Assembly Compatibility:
  • 10
    INCOMPATIBLE WITH RFC[10]
    Illegal PstI site found at 79
    Illegal PstI site found at 281
    Illegal PstI site found at 295
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal PstI site found at 79
    Illegal PstI site found at 281
    Illegal PstI site found at 295
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    INCOMPATIBLE WITH RFC[23]
    Illegal PstI site found at 79
    Illegal PstI site found at 281
    Illegal PstI site found at 295
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal PstI site found at 79
    Illegal PstI site found at 281
    Illegal PstI site found at 295
  • 1000
    COMPATIBLE WITH RFC[1000]


Design Notes

Firstly, we use profile-HMM algorithm instead of BLAST local alignment algorithm. To obtain PETase-related protein sequences from all species, Pfam entries and HMMER web server were used to search Swiss-prot and NCBI public databases. Then we set up a database of PETase protein sequences by selecting relatively strict sequences according to e-value, and manually adding sequences identified by homology. Finally, the phylogenetic tree was established through the ML algorithm of fireprot server, and several ancestor sequences of PETase were obtained according to the evolved nodes, among which the most primitive sequence was node 100.


Source

It does not come from any genomic sequence.

References