Objects of class
Assessment and either
DataMap or subclass
Mycobacterium tuberculosis strain H37Rv
1 2 3 4 5
All 5 objects have a list structure. For specifics on what the two
Assessment objects contain, please see the AssessORF
'H37Rv_PreSaved_DataMapObj' is an object of subclass
'H37Rv_PreSaved_ResultsObj_Genbank' is an object of subclass
Results with predicted genes from the Genbank databse.
'H37Rv_PreSaved_ResultsObj_GeneMarkS2' is an object of subclass
Results with predicted genes from the program GeneMarkS-2.
'H37Rv_PreSaved_ResultsObj_Glimmer' is an object of subclass
Results with predicted genes from the program Glimmer.
'H37Rv_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.
Species: M. tuberculosis
The mapping object, 'H37Rv_PreSaved_DataMapObj', stores the mapping of
proteomics evidence and evolutionary conservation evidence to the strain's
genome. The raw proteomics mass spectra data came from ProteomeXchange
dataset PXD006117. The related genomes used to determine evolutionary
conservation all came from the genus Mycobacterium, and links to their
sequences were downloaded from NCBI's Genome Browser. The object was built
MapAssessmentData function from the AssessORF
The 4 results objects, 'H37Rv_PreSaved_ResultsObj_Genbank',
'H37Rv_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
from the AssessORF package, a set of genes, and the mapping object
For the Genbank object, the genes were downloaded from the corresponding record in the Genbank database. For the other three objects, GenemarkS-2, 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.
GeneRightPos, and the
within each of the four results objects provide positional information on
the set of predicted genes used to generate that object.
GeneSource list item within each of the four results objects
describes where the predicted genes came from (either "Genbank",
"GeneMarkS2", "Glimmer", or "Prodigal" respectively).
SaveGenomeToPath("H37Rv", <INSERT FILE PATH HERE>) to save
the genome sequence for the strain to your local machine.
NCBI's Genome Browser: https://www.ncbi.nlm.nih.gov/genome/browse/#!/prokaryotes/
Genbank record: https://www.ncbi.nlm.nih.gov/nuccore/AL123456.3
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