Interface Summary Interface Description AlignmentStatsInterface AlignmentStats specifies the interface for an object that computes statistics of an Alignment. Class Summary Class Description AlignmentClass Alignment encapsulates the result of a sequence alignment between a query sequence and a subject sequence. AlignmentPrinterClass AlignmentPrinter provides an object that prints an Alignment. Blosum62Class Blosum62 provides the BLOSUM-62 substitution matrix for protein sequence alignment. DefaultAlignmentStatsClass DefaultAlignmentStats provides an object that computes statistics of an Alignment. FindProteinHybClass FindProteinHyb is a hybrid parallel program that finds matches for a protein in a protein sequence database. FindProteinHyb2Class FindProteinHyb2 is a hybrid parallel program that finds matches for a protein in a protein sequence database. FindProteinSeqClass FindProteinSeq is a sequential program that finds matches for a protein in a protein sequence database. ProteinDatabaseClass ProteinDatabase encapsulates a protein sequence database stored in a file. ProteinLocalAlignmentClass ProteinLocalAlignment is the abstract base class for an object that does local alignments of ProteinSequences. ProteinLocalAlignmentSeqClass ProteinLocalAlignmentSeq provides an object that does local alignments of ProteinSequences. ProteinLocalAlignmentSmpClass ProteinLocalAlignmentSmp provides an object that does local alignments of ProteinSequences. ProteinSequenceClass ProteinSequence encapsulates a protein sequence. SequenceClass Sequence is the abstract base class for a biological sequence.
Package edu.rit.compbio.seq Description
Package edu.rit.compbio.seq contains parallel programs for biological sequence alignment.
The following programs search a protein sequence database to find matches for a query protein sequence:
The following class encapsulates a protein sequence database; it includes a main program that prepares a database index file used by the above protein sequence database search programs:
- Class ProteinDatabase
The other classes are used by the above programs.
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