Version Compatibility

Reference examples tested with: BioPython 1.83+, Entrez Direct 21.0+

Before using code patterns, verify installed versions match. If versions differ:

• Python:

  pip show <package>

  then

  help(module.function)

  to check signatures

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Entrez Fetch

"Download a sequence from NCBI" → Retrieve a record by accession from an NCBI database and parse it into a usable object.

• Python:

  Entrez.efetch()

  +

  SeqIO.read()

  (BioPython)
• CLI:

  efetch -db nucleotide -id NM_007294 -format fasta

  (Entrez Direct)
• R:

  entrez_fetch()

  (rentrez)

Retrieve records from NCBI databases using Biopython's Entrez module (EFetch, ESummary utilities).

Required Setup

from Bio import Entrez

Entrez.email = 'your.email@example.com'  # Required by NCBI
Entrez.api_key = 'your_api_key'          # Optional, raises rate limit 3->10 req/sec

Core Functions

Entrez.efetch() - Retrieve Full Records

Fetch complete records in various formats from any NCBI database.

# Fetch GenBank record by ID
handle = Entrez.efetch(db='nucleotide', id='NM_007294', rettype='gb', retmode='text')
genbank_text = handle.read()
handle.close()

# Fetch FASTA sequence
handle = Entrez.efetch(db='nucleotide', id='NM_007294', rettype='fasta', retmode='text')
fasta_text = handle.read()
handle.close()

# Fetch multiple records
handle = Entrez.efetch(db='nucleotide', id='NM_007294,NM_000059', rettype='fasta', retmode='text')

Key Parameters:

db

'nucleotide'

'protein'

'pubmed'

id

'NM_007294'

'123,456,789'

rettype

'fasta'

'gb'

'abstract'

retmode

'text'

'xml'

retstart

0

retmax

20

WebEnv

query_key

Common Return Types by Database

Nucleotide/Protein:

'fasta'

'text'

'gb'

'text'

'gp'

'text'

'gbwithparts'

'text'

'seqid'

'text'

'acc'

'text'

PubMed:

'abstract'

'text'

'medline'

'text'

'xml'

'xml'

Gene:

'gene_table'

'text'

'xml'

'xml'

Entrez.esummary() - Document Summaries

Get brief summaries without downloading full records. Faster than efetch.

# Get summary for nucleotide record
handle = Entrez.esummary(db='nucleotide', id='NM_007294')
record = Entrez.read(handle)
handle.close()

summary = record[0]  # First (only) record
print(f"Title: {summary['Title']}")
print(f"Length: {summary['Length']}")
print(f"Organism: {summary['Organism']}")

Common Summary Fields:

# Nucleotide/Protein
summary['Title']          # Record title/description
summary['Caption']        # Short identifier
summary['Length']         # Sequence length
summary['Organism']       # Source organism
summary['TaxId']          # Taxonomy ID
summary['AccessionVersion']  # Full accession.version

# PubMed
summary['Title']          # Article title
summary['AuthorList']     # Authors
summary['Source']         # Journal
summary['PubDate']        # Publication date
summary['DOI']            # Digital Object Identifier

Parsing with Biopython

Parse into SeqRecord Objects

from Bio import Entrez, SeqIO

Entrez.email = 'your.email@example.com'

# Parse GenBank into SeqRecord
handle = Entrez.efetch(db='nucleotide', id='NM_007294', rettype='gb', retmode='text')
record = SeqIO.read(handle, 'genbank')
handle.close()

print(f"ID: {record.id}")
print(f"Length: {len(record.seq)}")
print(f"Features: {len(record.features)}")

# Parse FASTA into SeqRecord
handle = Entrez.efetch(db='nucleotide', id='NM_007294', rettype='fasta', retmode='text')
record = SeqIO.read(handle, 'fasta')
handle.close()

Parse Multiple Records

# Fetch multiple as FASTA
handle = Entrez.efetch(db='nucleotide', id='NM_007294,NM_000059,NM_000546', rettype='fasta', retmode='text')
records = list(SeqIO.parse(handle, 'fasta'))
handle.close()

for record in records:
    print(f"{record.id}: {len(record.seq)} bp")

Parse XML with Entrez.read()

# For structured data, use XML mode
handle = Entrez.efetch(db='gene', id='672', retmode='xml')
records = Entrez.read(handle)
handle.close()

# Navigate nested structure
gene = records[0]
print(f"Gene: {gene['Entrezgene_gene']['Gene-ref']['Gene-ref_locus']}")

Code Patterns

Fetch Sequence by Accession

from Bio import Entrez, SeqIO

Entrez.email = 'your.email@example.com'

def fetch_sequence(accession, db='nucleotide'):
    handle = Entrez.efetch(db=db, id=accession, rettype='fasta', retmode='text')
    record = SeqIO.read(handle, 'fasta')
    handle.close()
    return record

seq = fetch_sequence('NM_007294')
print(f"{seq.id}: {seq.seq[:50]}...")

Fetch GenBank with Features

def fetch_genbank(accession):
    handle = Entrez.efetch(db='nucleotide', id=accession, rettype='gb', retmode='text')
    record = SeqIO.read(handle, 'genbank')
    handle.close()
    return record

gb = fetch_genbank('NM_007294')
for feature in gb.features:
    if feature.type == 'CDS':
        print(f"CDS: {feature.location}")
        print(f"Product: {feature.qualifiers.get('product', ['?'])[0]}")

Fetch PubMed Abstract

def fetch_abstract(pmid):
    handle = Entrez.efetch(db='pubmed', id=pmid, rettype='abstract', retmode='text')
    abstract = handle.read()
    handle.close()
    return abstract

abstract = fetch_abstract('35412348')
print(abstract)

Get Record Summaries

def get_summaries(db, ids):
    if isinstance(ids, list):
        ids = ','.join(ids)
    handle = Entrez.esummary(db=db, id=ids)
    records = Entrez.read(handle)
    handle.close()
    return records

summaries = get_summaries('nucleotide', ['NM_007294', 'NM_000059'])
for s in summaries:
    print(f"{s['Caption']}: {s['Title'][:50]}... ({s['Length']} bp)")

Search Then Fetch

Goal: Find records matching a query and download their sequences in one workflow.

Approach: Search with

esearch

efetch

Reference (BioPython 1.83+):

handle = Entrez.esearch(db='nucleotide', term='human[orgn] AND insulin[gene] AND mRNA[fkey]', retmax=5)
search_results = Entrez.read(handle)
handle.close()

ids = search_results['IdList']

handle = Entrez.efetch(db='nucleotide', id=','.join(ids), rettype='fasta', retmode='text')
records = list(SeqIO.parse(handle, 'fasta'))
handle.close()

for record in records:
    print(f"{record.id}: {len(record.seq)} bp")

Fetch Protein by Gene ID

Goal: Retrieve protein sequences for a gene, navigating from gene symbol to protein database.

Approach: Search the gene database by symbol, use

elink

Reference (BioPython 1.83+):

handle = Entrez.esearch(db='gene', term='BRCA1[sym] AND human[orgn]')
result = Entrez.read(handle)
handle.close()
gene_id = result['IdList'][0]

handle = Entrez.elink(dbfrom='gene', db='protein', id=gene_id)
links = Entrez.read(handle)
handle.close()

protein_ids = [link['Id'] for link in links[0]['LinkSetDb'][0]['Link'][:3]]

handle = Entrez.efetch(db='protein', id=','.join(protein_ids), rettype='fasta', retmode='text')
proteins = list(SeqIO.parse(handle, 'fasta'))
handle.close()

Save Fetched Records to File

def download_sequences(ids, output_file, db='nucleotide', format='fasta'):
    handle = Entrez.efetch(db=db, id=','.join(ids), rettype=format, retmode='text')
    with open(output_file, 'w') as out:
        out.write(handle.read())
    handle.close()

download_sequences(['NM_007294', 'NM_000059'], 'brca_genes.fasta')

Common Errors

HTTPError 400

HTTPError 429

ValueError

ExpatError

retmode='text'

Decision Tree

Need to retrieve NCBI records?
├── Need full sequence?
│   └── Use efetch with rettype='fasta'
├── Need sequence + annotations?
│   └── Use efetch with rettype='gb' (GenBank)
├── Just need metadata (length, organism)?
│   └── Use esummary (faster)
├── Need PubMed abstract?
│   └── Use efetch with rettype='abstract'
├── Need structured data for parsing?
│   └── Use efetch with retmode='xml' + Entrez.read()
├── Downloading many records?
│   └── See batch-downloads skill
└── Need records from multiple databases?
    └── See entrez-link skill first

Related Skills

• entrez-search - Find record IDs before fetching
• entrez-link - Find related records in other databases
• batch-downloads - Download large numbers of records efficiently
• sequence-io/read-sequences - Parse downloaded sequences with SeqIO