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LoVis4u: a locus visualization tool for comparative genomics and coverage profiles

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  • معلومة اضافية
    • Contributors:
      Lund University, Profile areas and other strong research environments, Strategic research areas (SRA), eSSENCE: The e-Science Collaboration, Lunds universitet, Profilområden och andra starka forskningsmiljöer, Strategiska forskningsområden (SFO), eSSENCE: The e-Science Collaboration, Originator; Lund University, Faculty of Medicine, Department of Experimental Medical Science, Protein Evolution, Lunds universitet, Medicinska fakulteten, Institutionen för experimentell medicinsk vetenskap, Proteinevolution, Originator
    • نبذة مختصرة :
      Comparative genomic analysis often involves visualization of alignments of genomic loci. While several software tools are available for this task, ranging from Python and R libraries to stand-alone graphical user interfaces, a tool is lacking that offers fast, automated usage and the production of publication-ready vector images. Here we present LoVis4u, a command-line tool and Python API designed for highly customizable and fast visualization of multiple genomic loci. LoVis4u generates vector images in PDF format based on annotation data from GenBank or GFF files. It is capable of visualizing entire genomes of bacteriophages as well as plasmids and user-defined regions of longer prokaryotic genomes. Additionally, LoVis4u offers optional data processing steps to identify and highlight accessory and core genes in input sequences. Finally, LoVis4u supports the visualization of genomic signal track profiles from sequencing experiments. LoVis4u is implemented in Python3 and runs on Linux and MacOS. The command-line interface covers most practical use cases, while the provided Python API allows usage within a Python program, integration into external tools, and additional customization.