|Annotations of viral and phage genomes obtained by the GeneMark gene prediction programs (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
University of Rochester Online Lectures