JDet: interactive calculation and visualization of function-related conservation patterns in multiple sequence alignments and structures

• Published in: Bioinformatics 2012-02, Vol.28 (4), p.584-586
• Main Authors: Muth, Thilo, García-Martín, Juan A., Rausell, Antonio, Juan, David, Valencia, Alfonso, Pazos, Florencio
• Format: Article
• Language: English
• Subjects: Amino Acid Sequence; Biological and medical sciences; Fundamental and applied biological sciences. Psychology; General aspects; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects); Models, Molecular; Molecular Sequence Data; Proteins - chemistry; Proteins - genetics; Sequence Alignment; Software
• ISSN: 1367-4803; 1460-2059; 1367-4811
• DOI: 10.1093/bioinformatics/btr688

We have implemented in a single package all the features required for extracting, visualizing and manipulating fully conserved positions as well as those with a family-dependent conservation pattern in multiple sequence alignments. The program allows, among other things, to run different methods for extracting these positions, combine the results and visualize them in protein 3D structures and sequence spaces. Availability and implementation: JDet is a multiplatform application written in Java. It is freely available, including the source code, at http://csbg.cnb.csic.es/JDet. The package includes two of our recently developed programs for detecting functional positions in protein alignments (Xdet and S3Det), and support for other methods can be added as plug-ins. A help file and a guided tutorial for JDet are also available. Contact: [e-mail]