Originally designed as a set of
upgrades for the STARS package,
Phineus has been developed as a generic tool aimed
at addressing the existing and emerging requirements
for projects in which the same gene fragments are
sequenced from large numbers of strains of bacteria
or other organisms (e.g. multilocus sequence typing
(MLST), multilocus sequence analysis (MLSA) or phylogenetic
studies),
Phineus is designed to provide
a single piece of software which allows a laboratory
scientist to retrieve their chromatograms, and perform
all the steps needed to retrieve the trimmed
sequences needed for further analysis.
Phineus can be used for
a number of applications, but has considerable advantages
for MLST-like projects, as it interacts with MLST
internet databases so that the process of chromatogram
processing to allele and sequence type assignment
can be automated.
The software has been designed with flexibility
in mind, and is applicable to both large-scale,
and smaller projects. Phineus also features a user-friendly
interface, and has been designed to be easy to install
on a PC running Windows (although it also runs on
Linux or MacOS X).
| |
| Ease of use and install |
Intuitive menu-driven interface
and wizard based installation. |
| Platform independent |
Windows, Mac OS X and Linux (currently Windows
Vista not supported) |
| Easy administration |
Allowing System administrators to curate instances
of Phineus for multiple users. |
| Distributed architecture |
Phineus can be used as a 'client' to connect
to databases held on a users machine, a local
network or a remote server. |
| |
| Features |
| Chromatogram import |
Trace files can be imported from network, local
fixed or removable drives |
| Plate processing |
Multiple 96-well plates can be imported and
processed at one time. |
| Sequence editing |
Automatic reverse complementing to compare
traces in both directions, extraction of sequence
and allele and ST assignment for MLST projects. |
| Clipping module |
sequence clipping module optimised for MLST
and MLST-like projects. |
| Data storage |
All data backed up and stored locally, strain
information can be stored and all data available
for review and editing through intuitive interfaces |
| 3rd party analysis |
eBURST included with Phineus |
| Data export |
All data available for export in a variety
of formats for utilisation. |
| Schemas |
pre-configured settings for databases located
at http://www.mlst.net |
| Technical |
|
| JAVA |
GUI and main program written in JAVA |
| PERL |
Internal modules |
| SOAP |
SOAP interface to http://www.mlst.net allows
allele and ST assignment. |
| |
|
Over the next few pages, some of these areas and the solutions employed in Phineus are examined in slightly greater depth.
