The purpose of the Probabilistic Annotation service is to provide users with alternative annotations for genes, each attached to a likelihood score, and to translate these likelihood scores into likelihood scores for the existence of reactions in metabolic models. With the Probabilistic Annotation service:

• Users can quickly assess the quality of an annotation.

• Reaction likelihood computations allow users to estimate the quality of metabolic networks generated using the automated reconstruction tools in other services.

• Combining reaction likelihoods with gap filling both directly incorporates available genetic evidence into the gap filling process and provides putative gene annotations automatically, reducing the effort needed to search for evidence for gap filled reactions.

Details on the algorithm available in Likelihood-Based Gene Annotations for Gap Filling and Quality Assessment in Genome-Scale Metabolic Models

The Probabilistic Annotation server supports the following configuration variables:

• default_url: The default URL for this server's service endpoint.
• cdmi_url: URL for the central data model interface service endpoint. The CDMI service is used to build the static database files.
• shock_url: URL for the Shock service endpoint. The Shock service is used to store the static database files in a common location.
• workspace_url: URL for the Workspace service endpoint. The Workspace service is used to store typed objects created by the service.
• fbamodeling_url: URL for the FBA Modeling service endpoint. The FBA Modeling service is used to map roles to reactions when using model templates.
• userandjobstate_url: URL of the User and Job State service endpoint. The UJS service is used to manage the jobs that create ProbAnno typed objects.
• work_folder_path: Path to work folder containing sub-folders for running service. requests. The intermediate files created by the annotate() and calculate() methods are stored in this location.
• data_folder_path: Path to data folder containing static database files. A server can use different static database files by using different locations.
• load_data_option: Control how static database files are handled when starting service. Valid values are "shock" to load static files from Shock or 'preload' to use preloaded static database files.
• separator: Character string not found in any roles and used as separator between elements in lists. Default value is '///'.
• dilution_percent: Percentage of the maximum likelihood to use as a threshold to consider other genes as having a particular function aside from the one with greatest likelihood. Default value is 80.
• pseudo_count: Value used to dilute the likelihoods of annotations for annotations with weak homology to the query. Default value is 40.
• search_program: Search program for getting log scores of query genes in organism against all genes in high-confidence gene annotation database. Valid values are "blastp" or "usearch". Default value is "blastp".
• search_program_path: Path to search program. Use a fully-qualified path name.
• blast_threads: Number of threads to use when running search program.
• search_program_evalue: Value to use for the search program -evalue parameter. Default value is "1E-5".
• usearch_accel: Value to use for the -accel parameter of usearch program. The value is a number between 0 and 1 that tunes search speed against sensitivity. Default value is 0.33.