VOCS

VOCS organizes poxvirus genomic sequences and identifies orthologous gene clusters to support comparative genomics, functional annotation, and evolutionary analysis of poxviruses.

Key Features:

• Orthologous gene grouping: Automatic organization of orthologous genes into families based on BLASTP scores.
• Poxvirus sequence database: Repository of complete sequences of all known poxviruses that is regularly updated.
• Sequence similarity searches: Integration of BLASTP, BLASTX, and TBLASTN for sequence similarity and functional annotation.
• Multiple sequence alignment: Integration with Jalview for visualization and analysis of multiple sequence alignments.
• Dotplot analysis: Integration with Dotlet for dotplot visualization of sequence similarities and large-scale rearrangements.
• Local alignment: Integration with Laj for local alignment searches to detect regions of similarity.
• Nucleotide-to-amino-acid alignment: Integration with NAP for converting and aligning nucleotide sequences to amino acid sequences.
• Data querying: Support for complex SQL queries to extract specific DNA, protein sequences, and gene family datasets.
• Architecture: Java client-server implementation supporting database access and integrated analyses.

Scientific Applications:

• Evolutionary analysis: Identification of conserved and divergent orthologous gene families across poxvirus species.
• Comparative genomics: Detection of genomic rearrangements, duplications, and structural similarities using dotplots and alignments.
• Functional annotation: Annotation of poxvirus genes via BLASTP/BLASTX/TBLASTN similarity searches and alignment tools.
• Gene family studies: Extraction and analysis of specific gene families to study gene conservation, divergence, and evolutionary relationships.

Methodology:

Orthologous genes are grouped automatically using BLASTP scores; sequence similarity searches use BLASTP, BLASTX, and TBLASTN; multiple sequence alignment with Jalview, dotplot analysis with Dotlet, local alignment with Laj, and nucleotide-to-amino-acid alignment with NAP are available; a human database curator oversees the grouping and the system supports complex SQL queries for data extraction.