Package edu.rit.compbio.seq
Package edu.rit.compbio.seq
contains parallel programs
for biological sequence alignment.
See: Description
-
Interface Summary Interface Description AlignmentStats Interface AlignmentStats specifies the interface for an object that computes statistics of an Alignment. -
Class Summary Class Description Alignment Class Alignment encapsulates the result of a sequence alignment between a query sequence and a subject sequence.AlignmentPrinter Class AlignmentPrinter provides an object that prints an Alignment.Blosum62 Class Blosum62 provides the BLOSUM-62 substitution matrix for protein sequence alignment.DefaultAlignmentStats Class DefaultAlignmentStats provides an object that computes statistics of an Alignment.FindProteinHyb Class FindProteinHyb is a hybrid parallel program that finds matches for a protein in a protein sequence database.FindProteinHyb2 Class FindProteinHyb2 is a hybrid parallel program that finds matches for a protein in a protein sequence database.FindProteinSeq Class FindProteinSeq is a sequential program that finds matches for a protein in a protein sequence database.ProteinDatabase Class ProteinDatabase encapsulates a protein sequence database stored in a file.ProteinLocalAlignment Class ProteinLocalAlignment is the abstract base class for an object that does local alignments of ProteinSequences.ProteinLocalAlignmentSeq Class ProteinLocalAlignmentSeq provides an object that does local alignments of ProteinSequences.ProteinLocalAlignmentSmp Class ProteinLocalAlignmentSmp provides an object that does local alignments of ProteinSequences.ProteinSequence Class ProteinSequence encapsulates a protein sequence.Sequence Class 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:
- Class FindProteinSeq
- Class FindProteinHyb
- Class FindProteinHyb2
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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