TCH1516: 'Assessment' Objects for _Staphylococcus aureus_ subsp....
In DRK248/AssessORFData: Data and Files for the AssessORF Package

Description Usage Format Details Mapping object Results objects Getting the strain's genome Source

Objects of class Assessment and either subclass DataMap or subclass Results for Staphylococcus aureus subsp. aureus strain USA300_TCH1516

data(TCH1516_PreSaved_DataMapObj)
data(TCH1516_PreSaved_ResultsObj_GenBank)
data(TCH1516_PreSaved_ResultsObj_GeneMarkS2)
data(TCH1516_PreSaved_ResultsObj_Glimmer)
data(TCH1516_PreSaved_ResultsObj_Prodigal)

All 5 objects have a list structure. For specifics on what the two types of Assessment objects contain, please see the AssessORF package.

'TCH1516_PreSaved_DataMapObj' is an object of subclass DataMap.

'TCH1516_PreSaved_ResultsObj_GenBank' is an object of subclass Results with predicted genes from the GenBank database.

'TCH1516_PreSaved_ResultsObj_GeneMarkS2' is an object of subclass Results with predicted genes from the program GeneMarkS-2.

'TCH1516_PreSaved_ResultsObj_Glimmer' is an object of subclass Results with predicted genes from the program Glimmer.

'TCH1516_PreSaved_ResultsObj_Prodigal' is an object of subclass Results with predicted genes from the program Prodigal.

For all 5 objects, values of two key identifying list items within each object are listed below.

StrainID: TCH1516
Species: S. aureus

The mapping object, 'TCH1516_PreSaved_DataMapObj', stores the mapping of proteomics evidence and evolutionary conservation evidence to the strain's genome. The proteomics data was generated in-house and collected as part of the work for the AssessORF paper. The raw mass spectra data can be found at ProteomeXchange dataset PXD012538. The related genomes used to determine evolutionary conservation all came from the genus Staphylococcus, and links to their sequences were downloaded from NCBI's Genome Browser. The object was built using the MapAssessmentData function from the AssessORF package.

The 4 results objects, 'TCH1516_PreSaved_ResultsObj_GenBank', 'TCH1516_PreSaved_ResultsObj_GeneMarkS2', 'TCH1516_PreSaved_ResultsObj_Glimmer', and 'TCH1516_PreSaved_ResultsObj_Prodigal', store how much evidence there is supporting or against each gene in a set of predicted genes for the strain's genome. The four objects were built using the AssessGenes function from the AssessORF package, a set of genes, and the mapping object described here.

For the GenBank object, the genes were downloaded from the corresponding record in the GenBank database. For the other three objects, GenemarkS-2 (web server), Prodigal (2.6.3), and Glimmer (3.02) were run at default settings in order to generate the set of predicted genes for the corresponding results object.

The GeneLeftPos, GeneRightPos, and the GeneStrand within each of the four results objects provide positional information on the set of predicted genes used to generate that object.

The GeneSource list item within each of the four results objects describes where the predicted genes came from (either "GenBank", "GeneMarkS2", "Glimmer", or "Prodigal" respectively).

Use SaveGenomeToPath("TCH1516", <INSERT FILE PATH HERE>) to save the genome sequence for the strain to your local machine.

Proteomcis data: http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD012538

NCBI's Genome Browser: https://www.ncbi.nlm.nih.gov/genome/browse/#!/prokaryotes/

GenBank record: https://www.ncbi.nlm.nih.gov/nuccore/CP000730.1

DRK248/AssessORFData documentation built on Feb. 2, 2020, 11:06 p.m.