【Biopython】コドン表の表示と各生物のコドン表を使った翻訳方法[Python]

from Bio.Data import CodonTable

print(CodonTable.standard_dna_table)

実行結果
Table 1 Standard, SGC0

  |  T      |  C      |  A      |  G      |
--+---------+---------+---------+---------+--
T | TTT F   | TCT S   | TAT Y   | TGT C   | T
T | TTC F   | TCC S   | TAC Y   | TGC C   | C
T | TTA L   | TCA S   | TAA Stop| TGA Stop| A
T | TTG L(s)| TCG S   | TAG Stop| TGG W   | G
--+---------+---------+---------+---------+--
C | CTT L   | CCT P   | CAT H   | CGT R   | T
C | CTC L   | CCC P   | CAC H   | CGC R   | C
C | CTA L   | CCA P   | CAA Q   | CGA R   | A
C | CTG L(s)| CCG P   | CAG Q   | CGG R   | G
--+---------+---------+---------+---------+--
A | ATT I   | ACT T   | AAT N   | AGT S   | T
A | ATC I   | ACC T   | AAC N   | AGC S   | C
A | ATA I   | ACA T   | AAA K   | AGA R   | A
A | ATG M(s)| ACG T   | AAG K   | AGG R   | G
--+---------+---------+---------+---------+--
G | GTT V   | GCT A   | GAT D   | GGT G   | T
G | GTC V   | GCC A   | GAC D   | GGC G   | C
G | GTA V   | GCA A   | GAA E   | GGA G   | A
G | GTG V   | GCG A   | GAG E   | GGG G   | G
--+---------+---------+---------+---------+--

from Bio.Data import CodonTable

tablename = CodonTable.unambiguous_dna_by_name

for name in tablename.keys():
    print(name)

実行結果
Standard
SGC0
Vertebrate Mitochondrial
SGC1
Yeast Mitochondrial
SGC2
Mold Mitochondrial
Protozoan Mitochondrial
Coelenterate Mitochondrial
Mycoplasma
Spiroplasma
SGC3
Invertebrate Mitochondrial
SGC4
Ciliate Nuclear
Dasycladacean Nuclear
Hexamita Nuclear
SGC5
Echinoderm Mitochondrial
Flatworm Mitochondrial
SGC8
Euplotid Nuclear
SGC9
Bacterial
Archaeal
Plant Plastid
Alternative Yeast Nuclear
Ascidian Mitochondrial
Alternative Flatworm Mitochondrial
Blepharisma Macronuclear
Chlorophycean Mitochondrial
Trematode Mitochondrial
Scenedesmus obliquus Mitochondrial
Thraustochytrium Mitochondrial
Pterobranchia Mitochondrial
Candidate Division SR1
Gracilibacteria
Pachysolen tannophilus Nuclear
Karyorelict Nuclear
Condylostoma Nuclear
Mesodinium Nuclear
Peritrich Nuclear
Blastocrithidia Nuclear
Balanophoraceae Plastid
Cephalodiscidae Mitochondrial

from Bio.Data import CodonTable

print(CodonTable.unambiguous_dna_by_name["Standard"])
print(CodonTable.unambiguous_dna_by_name["Invertebrate Mitochondrial"])

実行結果
Table 1 Standard, SGC0

  |  T      |  C      |  A      |  G      |
--+---------+---------+---------+---------+--
T | TTT F   | TCT S   | TAT Y   | TGT C   | T
T | TTC F   | TCC S   | TAC Y   | TGC C   | C
T | TTA L   | TCA S   | TAA Stop| TGA Stop| A
T | TTG L(s)| TCG S   | TAG Stop| TGG W   | G
--+---------+---------+---------+---------+--
C | CTT L   | CCT P   | CAT H   | CGT R   | T
C | CTC L   | CCC P   | CAC H   | CGC R   | C
C | CTA L   | CCA P   | CAA Q   | CGA R   | A
C | CTG L(s)| CCG P   | CAG Q   | CGG R   | G
--+---------+---------+---------+---------+--
A | ATT I   | ACT T   | AAT N   | AGT S   | T
A | ATC I   | ACC T   | AAC N   | AGC S   | C
A | ATA I   | ACA T   | AAA K   | AGA R   | A
A | ATG M(s)| ACG T   | AAG K   | AGG R   | G
--+---------+---------+---------+---------+--
G | GTT V   | GCT A   | GAT D   | GGT G   | T
G | GTC V   | GCC A   | GAC D   | GGC G   | C
G | GTA V   | GCA A   | GAA E   | GGA G   | A
G | GTG V   | GCG A   | GAG E   | GGG G   | G
--+---------+---------+---------+---------+--
Table 5 Invertebrate Mitochondrial, SGC4

  |  T      |  C      |  A      |  G      |
--+---------+---------+---------+---------+--
T | TTT F   | TCT S   | TAT Y   | TGT C   | T
T | TTC F   | TCC S   | TAC Y   | TGC C   | C
T | TTA L   | TCA S   | TAA Stop| TGA W   | A
T | TTG L(s)| TCG S   | TAG Stop| TGG W   | G
--+---------+---------+---------+---------+--
C | CTT L   | CCT P   | CAT H   | CGT R   | T
C | CTC L   | CCC P   | CAC H   | CGC R   | C
C | CTA L   | CCA P   | CAA Q   | CGA R   | A
C | CTG L   | CCG P   | CAG Q   | CGG R   | G
--+---------+---------+---------+---------+--
A | ATT I(s)| ACT T   | AAT N   | AGT S   | T
A | ATC I(s)| ACC T   | AAC N   | AGC S   | C
A | ATA M(s)| ACA T   | AAA K   | AGA S   | A
A | ATG M(s)| ACG T   | AAG K   | AGG S   | G
--+---------+---------+---------+---------+--
G | GTT V   | GCT A   | GAT D   | GGT G   | T
G | GTC V   | GCC A   | GAC D   | GGC G   | C
G | GTA V   | GCA A   | GAA E   | GGA G   | A
G | GTG V(s)| GCG A   | GAG E   | GGG G   | G
--+---------+---------+---------+---------+--

from Bio import SeqIO

for record in SeqIO.parse("AAA27722.1.fasta", "fasta"):
    DNA_seq =record.seq
    print(DNA_seq.translate())
    print(DNA_seq.translate(table="Invertebrate Mitochondrial"))

実行結果
MSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFSYG
VQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFYKDDGNYKSRAEVKFEGDTLVNRIELKGIDFKEDG
NILGHKMEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYL
STQSALSKDPNEKRDHMILLEFVTAAGITHGMDELYK*
MSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFSYG
VQCFSSYPDHMKQHDFFKSAMPEGYVQESTMFYKDDGNYKSRAEVKFEGDTLVNSIELKGIDFKEDG
NILGHKMEYNYNSHNVYIMADKQKNGIKVNFKISHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYL
STQSALSKDPNEKSDHMILLEFVTAAGITHGMDELYK*

from Bio import SeqIO

for record in SeqIO.parse("AAA27722.1.fasta", "fasta"):
    DNA_seq =record.seq
    seq1 = DNA_seq.translate()
    seq2 = DNA_seq.translate(table="Invertebrate Mitochondrial")
    print(seq1.count("M"))
    print(seq2.count("M"))
    print(seq1.count("W"))
    print(seq2.count("W"))

実行結果
7
8
1
1