我正在使用 Python 创建一个程序，将一组 DNA 序列转换为氨基酸(蛋白质)序列。然后我需要找到一个特定的子序列，并计算出现这个特定子序列的序列数。这是我到目前为止的代码:
#Open cDNA_sequences file and read in line by line
with open('cDNA_sequences.csv', 'r') as results:
for line in results:
columns = line.rstrip("\n").split(",") #remove end of line characters and split commas to produce a list
ensemblID = columns[0] #ensemblID is first element in our list
dna_seq = columns[1] #dna_seq is second element in our list
genetic code = {
"UUU":"F", "UUC":"F", "UUA":"L", "UUG":"L",
"UCU":"S", "UCC":"s", "UCA":"S", "UCG":"S",
"UAU":"Y", "UAC":"Y", "UAA":"STOP", "UAG":"STOP",
"UGU":"C", "UGC":"C", "UGA":"STOP", "UGG":"W",
"CUU":"L", "CUC":"L", "CUA":"L", "CUG":"L",
"CCU":"P", "CCC":"P", "CCA":"P", "CCG":"P",
"CAU":"H", "CAC":"H", "CAA":"Q", "CAG":"Q",
"CGU":"R", "CGC":"R", "CGA":"R", "CGG":"R",
"AUU":"I", "AUC":"I", "AUA":"I", "AUG":"M",
"ACU":"T", "ACC":"T", "ACA":"T", "ACG":"T",
"AAU":"N", "AAC":"N", "AAA":"K", "AAG":"K",
"AGU":"S", "AGC":"S", "AGA":"R", "AGG":"R",
"GUU":"V", "GUC":"V", "GUA":"V", "GUG":"V",
"GCU":"A", "GCC":"A", "GCA":"A", "GCG":"A",
"GAU":"D", "GAC":"D", "GAA":"E", "GAG":"E",
"GGU":"G", "GGC":"G", "GGA":"G", "GGG":"G",} #genetic code, telling into which amino acids the DNA triplets translate
for i in range (0, len(dna_seq), 3):
codon = dna_seq[i:i+3]
protein += genetic_code [codon]
print (protein)
enterokinase_motif = "DDDDK"
proline_motif = "DDDDKP"
motif_number = 0
if enterokinase_motif in line:
motif_number = motif_number + 1;
elif proline_number in line:
motif_number = motif_number;
else:
motif_number = motif_number
print ("The number of sequences containing one or more enterokinase motifs is []".format(motif_number))
我在编写将 DNA 序列转换为蛋白质序列的代码时遇到了问题。
最佳答案
你应该阅读 Biopython .它带有与生物学和生物信息学相关的便利函数和类。
它有一个功能可以满足您的需求:Bio.Seq.translate
这里有代码示例:
>>> coding_dna = "GTGGCCATTGTAATGGGCCGCTGAAAGGGTGCCCGATAG"
>>> translate(coding_dna)
'VAIVMGR*KGAR*'
>>> translate(coding_dna, stop_symbol="@")
'VAIVMGR@KGAR@'
>>> translate(coding_dna, to_stop=True)
'VAIVMGR'
关于python - 如何使用python编程将一组DNA序列转换成蛋白质序列？，我们在Stack Overflow上找到一个类似的问题： https://stackoverflow.com/questions/40834338/