spa-typing

In this manual you will learn how to install the spa typing plugin in your BIONUMERICS database, how to import and assemble spa trace files, and how to screen sequences for known repeats and types downloaded from the Ridom/Seqnet SpaServer. Data can be submitted to the online server via a synchronization process and entries can be clustered based on the spa types.

In this tutorial we will perform some analyses on our imported Spa trace files: we will screen the trimmed consensus sequences for the repeat information and use this information to cluster and match our samples.

With the BIONUMERICS batch assembly import routine, hundreds of sequence trace files can be imported in batch and assembled automatically into contigs. This batch tool is very flexible and highly automated and allows the direct import of sequencer trace files from Applied BioSystems, Amersham and Beckman automated sequencers. In this tutorial you will learn how to use this batch tool by importing and assembling some Spa trace files.

The Spa typing plugin offers extra functionality to BIONUMERICS to do Spa typing for Staphylococcus aureus. Sequences in the database can be screened for known spa repeats and types downloaded from the SpaServer, data can be submitted to the SpaServer via a synchronization process, and entries can be clustered based on the spa types. In this tutorial the installation of the Spa typing plugin in a new database is covered.