[Computational Systems Biology Group @CNB-CSIC]

JDet Home

JDet is a multiplatform software for the interactive calculation and visualization of function-related conservation patterns in multiple sequence alignments and structures. It contains the set of tools and features we consider critical for the daily work with this kind of data, and that previously were disseminated in different packages and web servers. The package includes two of our recently developed programs for extracting this kind of information from protein alignments. JDet can be extended via plugins to implement other methods or parse their results.

For a general description of the package and the biological problem which prompted its development, as well as more information on multiple sequence alignments (MSAs), conserved positions, specificity determining positions (SDPs), etc., please take a look at the following article and the references cited there: Muth et al. (2011). Bioinformatics. doi: 10.1093/bioinformatics/btr688

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Documentation

Here you can find on-line versions of the user manual and the guided tutorial. These are also included in the dowloadable distribution.

References

Please cite the latest version of the following reference when reporting any data or image generated with the program:

Included software and licenses

JDet includes binary distributions of two functional residue detection programs:

JDet uses Java3DTM, for research and instructional Use

JDet also includes the Jmol plugin: Jmol: an open-source Java viewer for chemical structures in 3D. http://www.jmol.org/

Other third-party libraries are referenced in JDet's site at Google Code

Contact

For general questions/queries about the software, please contact Florencio Pazos (), for technical questions contact Juan A. Garcia Martin ().


[Computational Systems Biology Group @CNB-CSIC]