The most comprehensive database available for molecular biologists is GenBank, an open access resource that contains an annotated collection of all publicly available sequenced DNA and its translation into proteins. GenBank was founded by NCBI in 1982, and over the last three decades, the data it houses has grown exponentially, doubling every 18 months. As of August 2012, GenBank contained over 143 billion nucleobases.
Every sequence has a unique GenBank identifier that will directly retrieve its full sequence record. Here are some examples of database IDs:
CAA79696 NP_778203 263191547 BC043443 NM_002020
You can also search by submitter/author name in the format last_name first_initials (e.g., Smith JR). To search for an exact match, enclose it in quotation marks.
"contactin associated protein" "duchenne muscular dystrophy"
You can also restrict your search by using Boolean operators (AND, OR, NOT) as well as use specific subsets of records.
GenBank comprises several subdivisions:
Searching the Nucleotide database with general text queries will produce the most relevant results. You can also use a simple query based on protein name, gene name or gene symbol.
To limit your search to only certain kinds of records, you can search using GenBank's Limits4 page or alternatively use the Filter your results field to select categories of records after a search.
If you cannot find what you are searching for, check how the database interpreted your query by investigating the Search details field on the right side of the page. This field automatically translates your search into standard keywords.
For example, if you search for Drosophila, the Search details field will contain
Drosophila[All Fields]
and you will obtain all entries that mention Drosophila (including all its endosymbionts). You can restrict your search to only organisms belonging to the Drosophila genus by using a search tag and searching for
Drosophila[Organism]
Write a function recordCount that takes an organism name (string) as its first argument. The function also has a second optional parameter publicationDate that either takes a datetime.date object or a tuple of two datetime.date objects. The function must return the number of records that have been deposited in GenBank with the given organism name. If a single date is passed to the parameter publicationDate, the record count must be restricted to the records published at the given date. If a tuple containing two dates is passed to the parameter publicationDate, the record count must be restricted to the records published between the two given dates.
>>> from datetime import date >>> recordCount('Anthoxanthum') 84506 >>> recordCount('Anthoxanthum', publicationDate=date(2003, 8, 2)) 4 >>> recordCount('Anthoxanthum', publicationDate=(date(2003, 7, 25), date(2005, 12, 27))) 7 >>> recordCount('Stenosemella', publicationDate=(date(2000, 11, 9), date(2012, 8, 9))) 22
NCBI's databases, such as PubMed, GenBank, GEO, and many others, can be accessed via Entrez, a data retrieval system offered by NCBI. For direct access to Entrez, you can use Biopython's Bio.Entrez module.
The Bio.Entrez.esearch() function will search any of the NCBI databases. This function takes the following arguments:
We will now demonstrate a quick search for the rbcL gene in corn (Zea mays):
>>> from Bio import Entrez >>> Entrez.email = 'your_name@your_mail_server.com' >>> handle = Entrez.esearch(db='nucleotide', term='"Zea mays"[Organism] AND rbcL[Gene]') >>> record = Entrez.read(handle) >>> int(record['Count']) 6 # surely this value will change over time because GenBank is constantly updated
Note that when you request Entrez databases you must obey NCBI's requirements5: