使用蛋白质的基因标识符检索DNA序列

Question

我使用Biopython尝试检索与我拥有GI（71743840）的蛋白质相对应的DNA序列，这在NCBI页面上非常简单，我只需要查找refseq。 我的问题来自使用ncbi fetch实用程序在python中进行编码时，我找不到一种方法来检索有助于我进入DNA的任何字段。

handle = Entrez.efetch(db="nucleotide", id=blast_record.alignments[0].hit_id, rettype="gb", retmode="text")
seq_record=SeqIO.read(handle,"gb")

seq_record.features中有很多信息，但是必须有一种更简单且明显的方式来执行此操作，我们将不胜感激。 日Thnx！

Answer 1

您可以尝试访问SeqRecord的注释：

seq_record=SeqIO.read(handle,"gb")
nucleotide_accession = seq_record.annotations["db_source"]

在您的情况下， nucleotide_accession为“ REFSEQ：登录号NM_000673.4”

现在看看是否可以解析这些注释。 仅使用此测试用例：

nucl_id = nucleotide_accession.split()[-1]

handle = Entrez.efetch(db="nucleotide",
                       id=nucl_id,
                       rettype="gb",
                       retmode="text")
seq_record = SeqIO.read(handle, "gb")

Answer 2

您可以利用Entrez.elink，请求与核苷酸序列的UID相对应的蛋白质序列的UID：

from Bio import Entrez
from Bio import SeqIO
email = 'seb@free.fr'
term = 'NM_207618.2' #fro example, accession/version

### first step, we search for the nucleotide sequence of interest
h_search = Entrez.esearch(
        db='nucleotide', email=email, term=term)
record = Entrez.read(h_search)
h_search.close()

### second step, we fetch the UID of that nt sequence
handle_nt = Entrez.efetch(
        db='nucleotide', email=email, 
        id=record['IdList'][0], rettype='fasta') # here is the UID

### third and most important, we 'link' the UID of the nucleotide
# sequence to the corresponding protein from the appropriate database
results = Entrez.read(Entrez.elink(
        dbfrom='nucleotide', linkname='nucleotide_protein',
        email=email, id=record['IdList'][0]))

### last, we fetch the amino acid sequence
handle_aa = Entrez.efetch(
        db='protein', email=email, 
        id=results[0]['LinkSetDb'][0]['Link'][0]['Id'], # here is the key...
        rettype='fasta')