python - 如何使用 Biopython 查找蛋白质的核苷酸序列？

Question

我有一些蛋白质，我想找到它们相应的核苷酸序列。我还有发现该蛋白质的基因组。在基因组中，我找到了该蛋白质对应的基因ID。但是，我无法通过基因 ID 获取核苷酸序列。我尝试过使用 Entrez Efetch:

Entrez.email = "dddd@gmail.com"
with open("genome.gb", "w") as out_handle:
    request = Entrez.efetch(db="gene", id="2703488", rettype="gb", retmode="text")
    out_handle.write(request.read())
    request.close()

但这仅返回以下内容:

1. G
tail component [Escherichia virus Lambda]
Other Aliases: lambdap14
Other Designations: tail component
Annotation:  NC_001416.1 (9711..10133)
ID: 2703488

有没有办法使用 Efetch 获取实际的核苷酸序列？提前致谢!

Answer 1

您可以使用 Annotation: 行中的信息从 NCBI 核苷酸获取序列:

>>> from Bio import Entrez, SeqIO
>>> Entrez.email = ''
>>> request = Entrez.efetch(db="nuccore", id="NC_001416.1", rettype="fasta", seq_start="9711", seq_stop="10133")
>>> seq_record = SeqIO.read(request, "fasta")
>>> seq_record
SeqRecord(seq=Seq('ATGTTCCTGAAAACCGAATCATTTGAACATAACGGTGTGACCGTCACGCTTTCT...TGA', SingleLetterAlphabet()), id='NC_001416.1:9711-10133', name='NC_001416.1:9711-10133', description='NC_001416.1:9711-10133 Enterobacteria phage lambda, complete genome', dbxrefs=[])
>>> print(seq_record.seq)
ATGTTCCTGAAAACCGAATCATTTGAACATAACGGTGTGACCGTCACGCTTTCTGAACTGTCAGCCCTGCAGCGCATTGAGCATCTCGCCCTGATGAAACGGCAGGCAGAACAGGCGGAGTCAGACAGCAACCGGAAGTTTACTGTGGAAGACGCCATCAGAACCGGCGCGTTTCTGGTGGCGATGTCCCTGTGGCATAACCATCCGCAGAAGACGCAGATGCCGTCCATGAATGAAGCCGTTAAACAGATTGAGCAGGAAGTGCTTACCACCTGGCCCACGGAGGCAATTTCTCATGCTGAAAACGTGGTGTACCGGCTGTCTGGTATGTATGAGTTTGTGGTGAATAATGCCCCTGAACAGACAGAGGACGCCGGGCCCGCAGAGCCTGTTTCTGCGGGAAAGTGTTCGACGGTGAGCTGA