Data pertaining to all aspects
of an MLST project (user settings, organism specific
settings (loci used etc.) sequence data, allele
numbers and supplementary information) are stored
and managed within Phineus.
The main concepts
inherent in Phineus data management fall into 3
categories, Project data, Schema data and Pipeline
Data
Projects
Phineus provides a method of associating related
data long term, to aid in future analysis. A project
is a collection of settings used by Phineus to process
and organise chromatograms.
Projects enable a user
to process several datasets using identical settings,
and once the data is checked and saved, view all
the data associated with that project together, either
on a strain-by-strain or a microtitre plate-by-plate
basis.
For example a project
could be - 'MLST'
Schema
The first
component of a project is a Schema.
A schema describes all aspects relating
to a particular organism specific MLST/MLSA project.
- The number of loci used.
- A reference sequence for the whole gene fragment used to define alleles
- The length of the trimmed gene fragment
- A sequence for the 5' and 3' ends of the trimmed gene fragment
- An internal sequence used in an alternative trimming
method
- Coordinates for determining the 5' and 3' ends of the gene fragment using the internal
sequence
- The order of loci used to define the allelic profile
- The species name(s) for the organism(s) to which the schema corresponds
For example if the project being used is 'MLST'
an example of a Schema would be 'Streptococcus
pneumoniae'
Pipeline
A
Pipeline is a framework in which
Phineus processes a series of chromatograms and consists
of a series of modules (with their order
of execution and settings)
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