ArrayPlex: distributed, interactive and programmatic access to genome sequence, annotation, ontology, and analytical toolsets

Table 3 Command-line modules

Module name	Purpose	Class
AnnotationResources.jar	Genome annotation and ontology retrieval	Generic
DatasetOperations.jar	User dataset retrieval, transformation, and manipulation	Generic
SequenceAnalysis.jar	Genome sequence extraction, search, discovery, manipulation	Generic
ErrorModel.jar	Example routines in replicate combination	Regulation
InteractionGraph.jar	Example routines in network modelling	Regulation
TargetAnalysis.jar	Example routines in ontological and sequence analysis	Regulation

The six command-line modules built by and provided with the ArrayPlex installation. The first three modules, classified as 'Generic', are most useful for command-line access to any of the resources hosted on the ArrayPlex server. This includes all genome sequence, annotation, ontology, and user dataset information. The SequenceAnalysis.jar module additionally contains all of the genome sequence operations featured in the ArrayPlex client, including organism-specific sequence extraction, BLAST, known-motif search, de novo motif discovery, and multi-sequence alignment. The modules classified as 'Regulation' are useful for analysis of regulator-target relationships as illustrated in our recent reconstruction of a functional transcriptional regulatory network [21]. They provide reusable analytical operations and illustrate how the ArrayPlex programmatic API can be used for constructing novel analysis routines.

ISSN: 1474-760X