GenDBWiki/WebDocumentation/DialogWindows/SupportingObservationsUpdate
This method considers for a subset of the CDS-regions (of a contig) whether significant functional observations of a specified tool exist that are not yet used in the functional annotation of the CDS-regions.
Introduction
Supporting Observations: Functional Annotations of a region object (e.g. a CDS region) considerably rely on information that is provided by precomputed functional observations of various tools suitable to detect functional characteristics. For example Blast tools may detect homology information for a regions's sequence that allows you to infer some functional meaning of the region object (e.g. what kind of gene it is!). It's useful to list those related observations in the framework of the functional annotation. Observations listed as attributes of the annotation object are referred to as supporting observations. They serve to provide evidence to the content of the annotation.
This method serves two aspects in managing the supporting observations of the CDS-regions of a contig:
It may check for a subset of CDS regions and a specified tool whether observations of that tool exist that show better characteristics (Score and Evalue) than the supporting observations that are currently referred to from the functional annotations. The result is shown as a list where each row entry displays the necessary information about the considered gene, it's current functional annotation (including the best currently used supporting observation for that tool-if it exists) and finally the up-to-date most promising candidate observation to improve evidence of the annotation . A html-link allows you to get quickly into the annotation dialog of that gene.
Additionally it's possible to enrich the result-list by observations that are proposed as the currently best candidates to be used in the annotations when there haven't been used any supporting observations yet!
General settings
The CDS-regions will be taken from the contig, that is currently selected in the session!
Select from Blast-tools: Here you can choose a specific Blast tool from a list of all available Blast tools in the project's database.
Number of regions to be processed at once (size of interval): The programm will take this setting as the number of CDS-regions that are processed at once (called size of interval)!
Change stepping size: Here you can change the interval size.
Select range of CDS-regions to be processed: The overall set of CDS regions can be seen as a sorted list of genes [gene_1 ... gene_N] that is divided for computational reasons into a subset of intervals (e.g. when the interval size is 50 you will get intervals like gene_1 .. gene_50, gene_51 .. gene_100 and so on). This allows you to process small subsets of the genes in an ordered fashion!
Propose all: Check out this box if you want the programm to propose candidate observations for functional annotations even though there haven't been used any supporting observations so far! This helps you to complete genome annotation.
Compute results for settings: This will start the computation!
Interpreting the results
Following is an overview of the most important elements (column names) of the single entries in the result-list:
CDS_NAME: Examined gene. The name is also a link to the referred region in the main window of gendb.
CURRENT_BEST_EVALUE: Evalue of the best (currently used) supporting observation (corresponding to the specified tool).
CURRENT_BEST_SCORE: Score of the best (currently used) supporting observation (corresponding to the specified tool).
CURRENT_BEST_DESCR: Description of the best (currently used) supporting observation (corresponding to the specified tool).
CURRENT_BEST_DATE: Date of the best (currently used) supporting observation (corresponding to the specified tool).
CURRENT_AnnF_DESC: Description of the current annotation function.
CURRENT_AnnF_DATE: Date of creation of the current annotation function.
PROPOSED_EVALUE: Evalue of the proposed observation.
PROPOSED_SCORE: Score of the proposed observation.
PROPOSED_DESCR: Description of the proposed observation.
PROPOSED_DATE: Date of creation of the proposed observation.
ACTIONS: Opens the annotation dialog.
ANNOTATOR: Name of the annotator that created the current annotation function.