Package ubic.gemma.core.analysis.sequence
package ubic.gemma.core.analysis.sequence
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ClassDescriptionSupports obtaining detailed information about the sequence analysis of probes on microarrays.Given a set of BlatAssociations that might be redundant, clean them up and score them.Used to convert BlatResult objects into PSL lines that can be displayed in the UCSC Genome Browser.This is a convenience object to hold the results of CompositeSequence mapping results.Holds parameters for how mapping should be done.Provides methods for mapping sequences to genes and gene products.Scan sequences for repeats using RepeatMasker.Used to assign a bin to a chromosome location, identify bins for a range, or to generate SQL to add to a query on a GoldenPath database.Convenient methods for manipulating BioSequences and PhysicalLocationsTools for writing biosequences to files so they can be analyzed by external tools, and then read back into Gemma.Class to manage the gfServer and run BLAT searches.