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See:
Description
| Interface Summary | |
|---|---|
| AlignmentStats | Interface AlignmentStats specifies the interface for an object that computes statistics of an Alignment. |
| Class Summary | |
|---|---|
| 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 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:
The other classes are used by the above programs.
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