Welcome to classACNUC’s documentation!

Scope

The ACNUC biological sequence database system provides powerful and fast query and extraction capabilities to a variety of nucleotide and protein sequence databases. The collection of ACNUC databases includes the EMBL, GenBank, RefSeq, Etc. See the ACNUC website

The ACNUC biological sequence database system has been designed in order to allow most structured fields of sequence annotations to be used as potential entry points in the database and to be combined in complex queries.

The ACNUC query language allows expression and logical combination of retrieval criteria to elaborate arbitrarily complex queries. Each query creates the list of all matching database elements.

classACNUC is a Python class that tries to simplify the writing of the queries and the creation of the corresponding lists by automatizing much of the process behind. But this python class is also modifying the sequence extraction process to merge the desired informations extracted from the bank data (taxonomy, strains, lengths, position Etc.) in a compact form inside the FASTA description line. The resulting files are therefore more rapidly usable for further analysis or any use. This python class was initially designed for the riboDB website query and retrieval engine and it is also used in leBIBI-QBPP databases construction engine. classACNUC relies on the ACNUC Python API. See riboDB website for an application. It can be used with the ACNUC RiboDB, GenBank and EMBL databases.

Download

You can download classACNUC and the ACNUC Python API (please follows the instruction to compile the API).

classACNUC is distributed under the *ceCILL-C license*.

Note

The python module dateutil is mandatory ! (apt-get install python-dateutil as root).

Indices and tables