search

biotite.database.entrez.search(query, db_name, number=20)

Get all PDB IDs that meet the given query requirements, via the NCBI ESearch service.

This function requires an internet connection.

Parameters:

queryQuery

The search query.

db_namestr:

E-utility or common database name.

numberQuery

The maximum number of UIDs that are obtained.

Returns:

idslist of str

A list of strings containing all NCBI UIDs (accession number) that meet the query requirements.

Warning

Even if you give valid input to this function, in rare cases the database might return no or malformed data to you. In these cases the request should be retried. When the issue occurs repeatedly, the error is probably in your input.

Notes

A list of available search fields with description can be found here.

Examples

>>> query = SimpleQuery("Escherichia coli", "Organism") & \
...         SimpleQuery("90:100", "Sequence Length")
>>> ids = search(query, "nuccore", number=5)
>>> print(ids)
['...', '...', '...', '...', '...']

Gallery

Customized visualization of a multiple sequence alignment

Customized visualization of a multiple sequence alignment

Hydropathy and conservation of ion channels

Hydropathy and conservation of ion channels

Conservation of binding site

Conservation of binding site

Fetching and aligning a protein from different species

Fetching and aligning a protein from different species

Polymorphisms in a gene

Polymorphisms in a gene

Domains of bacterial sigma factors

Domains of bacterial sigma factors

Biotite color schemes for protein sequences

Biotite color schemes for protein sequences