Comparative genomics visualization made easy. GOTaxExplorer presents a new approach to comparative genomics that integrates functional information and families with the taxonomic classification. It integrates UniProt, Gene Ontology, NCBI Taxonomy, Pfam and SMART in one database. GOTaxExplorer provides four different query types:
1. selection of sets
2. comparison of sets of Pfam families
3. semantic comparison of sets of GO terms
4. functional comparison of sets of gene products

This permits to select custom sets of GO terms, families or taxonomic groups. For example, it is possible to compare arbitrarily selected organisms or groups of organisms from the taxonomic tree on the basis of the functionality of their genes. Furthermore, it enables to determine the distribution of specific molecular functions or protein families in the taxonomy.

The comparison of sets of GO terms allows to assess the semantic similarity of two different GO terms. The functional comparison of gene products makes it possible to identify functionally equivalent and functionally related gene products from two organisms on the basis of GO annotations and a semantic similarity measure for GO. This method is independent of sequence similarity and therefore capable of finding functionally equivalent or functionally related proteins that are not homologous.

GOTaxExplorer uses a simple query language. The graphical user interface contains facilities to help in the formulation of queries. The command line interface can be used in scripts to automate query execution and result handling. Furthermore, GOTaxExplorer allows to visualize results from GO and the taxonomy in a 2D tree representation or in a 3D graph view.

Please Note: this program is a Java Web Start Application, you need to right-click on the download file and choose "Launch".

Requirements:
* Java

The license of this software is Free, you can free download and free use this 3d graphic software.