the basic bioinformatic tools for viral genome analysis
Several fundamental bioinformatic instruments are frequently employed for viral genome study, including:
1. Viral genome sequences can be aligned with other sequences or with reference sequences using programmes for sequence alignment such as ClustalW, MUSCLE, or MAFFT.
2. Genes, gene products, and other characteristics of the viral genome can be identified using genome annotation tools like Prokka, GeneMark, or RAST.
3. Viral genome sequences can be assembled from raw sequencing reads using genome assembly software like SPAdes, ABySS, or Velvet.
4. To retrace the evolution of viral genomes, phylogenetic analysis methods like RAxML, PhyML, or BEAST can be utilised.
5. To detect genetic changes like single nucleotide polymorphisms (SNPs), insertions, or deletions in viral genome sequences, variant calling tools like VarScan, GATK, or FreeBayes can be utilised.
6. You can utilise visualisation tools like Circos, IGV, or Tablet to see how the genomic traits are distributed throughout the viral genome.
To examine viral genomes and learn more about their biology, evolution, and pathogenicity, these methods can be utilised singly or collectively.
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