Summary: The exploration and comparison of genome organization is routinely used in the frame of genomic and phylogenomic analyses. As a consequence, in the past few years, various tools allowing visualizing genomic contexts have been developed. However, their use is often hampered by a lack of flexibility, particularly concerning associated databases input formats and figure customization. Here we present GeneSpy, a graphical user interface that allows the visualization and dynamic exploration of eukaryotic and prokaryotic annotated genomes. GeneSpy relies on user-friendly manageable local databases and allows the easy customization and production of figures in a multitude of formats. Availability and implementation: GeneSpy is freely available at https://lbbe.univ-lyon1.fr/GeneSpy/ for Linux, Mac OS and Windows under CeCILL license (http://www.cecill.info/licences/). It is written in Python 2.7 and depends on Matplotlib, Tkinter and Sqlite libraries. Supplementary information: Supplementary data are available at Bioinformatics online.

MOTIVATION: Most of the protein tyrosine kinases found in bacteria have been recently classified in a new family, termed BY-kinase. Indeed, they share no sequence homology with their eukaryotic counterparts and have no known eukaryotic homologues. They are involved in several biological functions (e.g. capsule biosynthesis, antibiotic resistance, virulence mechanism). Thus, they can be considered interesting therapeutic targets to develop new drugs to treat infectious diseases. However, their identification is rendered difficult due to slow progress in their structural characterization and comes most often from biochemical experiments. Moreover BY-kinase sequences are related to many other bacterial proteins involved in several biological functions (e.g. ParA family proteins). Accordingly, their annotations in generalist databases, sequence analysis and classification remain partial and inhomogeneous and there is no bioinformatics resource dedicated to these proteins. RESULTS: The combination of similarity search with sequence-profile alignment, pattern matching and sliding window computation to detect the tyrosine cluster was used to identify BY-kinase sequences in UniProt Knowledgebase. Cross-validations with keywords searches, pattern matching with several patterns and checking of motifs conservation in multiple sequence alignments were performed. Our pipeline identified 640 sequences as BY-kinases and allowed the definition of a PROSITE pattern that is the signature of the BY-kinases. The sequences identified by our pipeline as BY-kinases share a good sequence similarity with BY-kinases that have already been biochemically characterized, and they all bear the characteristic motifs of the catalytic domain, including the three Walker-like motifs followed by a tyrosine cluster. AVAILABILITY: http://bykdb.ibcp.fr