biojava 6.0.0 API

Set of classes that responsible for providing APIs and Command Prompt access to generate some basic physico-chemical properties of protein sequences.

Set of classes that responsible for providing APIs access to generate some PROFEAT properties of protein sequences.

Set of classes that enable the conversion protein sequences into various attributes.

Set of classes that handles the reading and writing of xml files.

Set of classes that responsible for data handling.

FASTQ and variants sequence format I/O.

BioJava provide a module biojava-protein-disorder for prediction disordered regions from a protein sequence.

Classes for the alignment of structures.

Classes related to the implementation of the CE alignment algorithm, here called jCE.

This package deals with the server communication for auto-downloading pre-calculated alignments.

Classes related to the implementation of the FATCAT alignment algorithm, here called jFATCAT.

Utility methods for better interaction with Jmol.

Helper classes for structural alignment.

Classes for the pairwise alignment of structures.

Classes related to Java Web Start

Serialization and deserialization for structure alignment results (as AFPChain object) to XML.

Input and Output of Structures

Matrix package for from JAMA

Parsers and API for SCOP, Structural Classification of Proteins.

This package contains the interfaces that need to be implemented by discrete alignment services.