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Table 3 Command-line modules

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

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
  1. 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.