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我使用 Biopython 尝试检索与我有 GI（71743840）的蛋白质对应的 DNA 序列，从 NCBI 页面这很容易，我只需要查找 refseq。我的问题是在使用 ncbi 获取实用程序在 python 中编码时出现，我找不到一种方法来检索任何可以帮助我进入 DNA 的字段。

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，但必须有一种更简单明了的方法来做到这一点，任何帮助将不胜感激。谢谢！

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2 回答 2

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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是“REFSEQ：加入 NM_000673.4”

现在看看你是否可以解析这些注释。只有这个测试用例：

nucl_id = nucleotide_accession.split()[-1]

handle = Entrez.efetch(db="nucleotide",
                       id=nucl_id,
                       rettype="gb",
                       retmode="text")
seq_record = SeqIO.read(handle, "gb")
于 2014-11-05T08:03:51.603 回答
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您可以利用 Entrez.elink，请求与核苷酸序列的 UID 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')
于 2018-09-13T09:49:12.700 回答