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
Streptococcus pyogenes strain MGAS5005
1 2 3 4 5 |
All 5 objects have a list structure. For specifics on what the two
types of Assessment
objects contain, please see the AssessORF
package.
'MGAS5005_PreSaved_DataMapObj' is an object of subclass DataMap
.
'MGAS5005_PreSaved_ResultsObj_GenBank' is an object of subclass
Results
with predicted genes from the GenBank database.
'MGAS5005_PreSaved_ResultsObj_GeneMarkS2' is an object of subclass
Results
with predicted genes from the program GeneMarkS-2.
'MGAS5005_PreSaved_ResultsObj_Glimmer' is an object of subclass
Results
with predicted genes from the program Glimmer.
'MGAS5005_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
: MGAS5005
Species
: S. pyogenes
The mapping object, 'MGAS5005_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 PXD012568. The related genomes used to determine
evolutionary conservation all came from the family, Streptococcaceae
exculding anomalous genomes and non-complete Streptococcus pneumoniae
genomes. 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, 'MGAS5005_PreSaved_ResultsObj_GenBank',
'MGAS5005_PreSaved_ResultsObj_GeneMarkS2',
'MGAS5005_PreSaved_ResultsObj_Glimmer', and
'MGAS5005_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("MGAS5005", <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=PXD012568
NCBI's Genome Browser: https://www.ncbi.nlm.nih.gov/genome/browse/#!/prokaryotes/
GenBank record: https://www.ncbi.nlm.nih.gov/nuccore/CP000017.2
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