GeneMarkTM
VIOLIN
Annotations of viral and phage genomes obtained by the GeneMark gene prediction programs (VIOLIN)

VIOLIN:
SEARCH our database of annotated viruses and phages

Predict genes in viral genomes using GeneMark.hmm with heuristic models (for genomes of any size) or GeneMarkS (for larger genomes). While 1 Mb is the recommended sequence size for GeneMarkS, we have had success annotating viral genomes around 50 kb with this tool. There are two major issues with gene finding in viruses: overlapping genes (frequent) and introns (rare). Thus, the tools we use to annotate viral genomes are based on the prokaryotic version of GeneMark.hmm.

Useful Virus and Phage links
NCBI Entrez Genomes
Los Alamos STDGEN
VIDA
University of Rochester Online Lectures
Virology.net

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