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Sequence analysis is one of the major subjects of | Sequence analysis is one of the major subjects of | ||
bioinformatics. | [http://en.wikipedia.org/wiki/Bioinformatics bioinformatics]. | ||
Several existing libraries combine the representation of biological sequences with exact and approximate pattern matching as well as | Several existing libraries combine the representation of biological sequences with exact and approximate pattern matching as well as | ||
alignment algorithms. | alignment algorithms. | ||
We present Jstacs, an open source Java library, which focuses on the statistical analysis of biological sequences instead. Jstacs comprises an | We present Jstacs, an [http://en.wikipedia.org/wiki/Open_source open source] Java library, which focuses on the statistical analysis of biological sequences instead. Jstacs comprises an | ||
efficient representation of sequence data and provides implementations of many statistical models with generative and discriminative approaches | efficient representation of sequence data and provides implementations of many statistical models with generative and discriminative approaches | ||
for parameter learning. Using Jstacs, classifiers can be assessed and | for parameter learning. Using Jstacs, classifiers can be assessed and | ||
Revision as of 07:56, 2 September 2008
Jstacs
A Java framework for statistical analysis and classification of biological sequences
Sequence analysis is one of the major subjects of bioinformatics. Several existing libraries combine the representation of biological sequences with exact and approximate pattern matching as well as alignment algorithms. We present Jstacs, an open source Java library, which focuses on the statistical analysis of biological sequences instead. Jstacs comprises an efficient representation of sequence data and provides implementations of many statistical models with generative and discriminative approaches for parameter learning. Using Jstacs, classifiers can be assessed and compared on test datasets or by cross-validation experiments evaluating several performance measures. Due to its strictly object-oriented design Jstacs is easy to use and readily extensible.
Current release
You can download Jstacs version 1.0 here.
You find the API documentation for this release here.
