jstacs.de

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Ava framework for st. Lassification of biological s. 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 statisti...

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Ava framework for st. Lassification of biological s. 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 statisti...

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Main Page - Jstacs | jstacs.de Reviews

https://jstacs.de

Ava framework for st. Lassification of biological s. 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 statisti...

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jstacs.de

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FAQs - Jstacs

http://www.jstacs.de/index.php/FAQs

Reporting bugs and requesting new features. Also have a look at the code example Loading data. Q: How do I create an AlphabetContainer. Instance for DNA sequences? Container = new AlphabetContainer. Q: Why shall I use the AlphabetContainer. And not just a simple Alphabet. Because for some data you will not have the same alphabet at each position of the sequence, e.g. when using phenotypic data. Hence, we also strongly recommend to always use getAlphabetLengthAt(int). Q: How can I create a simple sequence?

2

TALgetter - Jstacs

http://www.jstacs.de/index.php/TALgetter

By Jan Grau, Annett Wolf, Maik Reschke, Ulla Bonas, Stefan Posch and Jens Boch. TALgetter allows you to scan input DNA sequences for putative target sites of a given TAL (transcription activator like) effector as typically expressed by many Xanthomonas. We provide TALgetter as a public web-server, a web-application that can be installed in a local Galaxy server, and as a command line program. Running the command line application. Large input data sets. If you use TALgetter, please cite. 9 (3), 2013.

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Generated Documentation (Untitled)

http://www.jstacs.de/api-1.5/index.html

This document is designed to be viewed using the frames feature. If you see this message, you are using a non-frame-capable web client. Link to Non-frame version.

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Dispom - Jstacs

http://www.jstacs.de/index.php/Dispom

By Jens Keilwagen, Jan Grau, Ivan A. Paponov, Stefan Posch, Marc Strickert and Ivo Grosse. Recently, we published Dimont a successor of Dispom. Dimont uses some heuristics and is hence much faster than Dipom. Typically it provides results within one hour for large data sets. If you are interested in Dimont please visit the project homepage. We find that the combination of searching for differentially abundant motifs and inferring a position distribution from the data is beneficial for de-novo motif disco...

5

Acknowledgements - Jstacs

http://www.jstacs.de/index.php/Acknowledgements

We thank the eclipse. Team for developing a wonderful IDE, which greatly accelerates the development of Jstacs. The development of Jstacs greatly profited from the following libraries. Numerical methods from JTEM. Was adapted from Sundar Dorai-Raj. Apache XML Graphics Commons. Jstacs was supported by the German Ministry of Education and Research (BMBF Grant No. 0312706A/D) within the Bioinformatics Centre Gatersleben - Halle. And by the Ministry of Culture, Saxony-Anhalt, grant XP3624/0606T.

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Supervised attribute relevance detection using cross comparison (SARDUX)

http://dig.ipk-gatersleben.de/sardux/sardux.html

Supervised Attribute Relevance Detection using Cross Comparisons (SARDUX). Supplementary information to the paper submitted to ASAI 2009. Towards matrix-based selection of feature pairs for efficient ADMET prediction. Marc Strickert, Axel J. Soto. Jens Keilwagen, and Gustavo E. Vazquez. Fig1: Exemplary relevance matrix of chemical compound attributes. Related to the prediction of the octanol-water partitioning coefficient. Red, yellow, blue indicate high, average, and low importance, respectively. The la...

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jstacs.de

Main Page - Jstacs

Ava framework for st. Lassification of biological s. 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 statisti...

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