The revolution in sequencing technologies improved quality, accuracy, and throughput and decreased cost and time of genome sequencing, which has now become a routine step of phage characterization. However, the accumulation of genomic data created an annotation bottleneck. Today, thousands of phage genomes are completely sequenced, deposited, and accessible; yet, converting these data into biological knowledge remains slow. Computers and computer scientists are continuously providing tools to overcome the hurdles of data visualization and analysis, but the rate-limiting step to genome interpretation remains human expertise needed for genome annotation and metadata curation. This part of the workshop will focus on this annotation process, which starts with a complete or partial DNA sequence and ends in an integrated model of the biology of an organism. Several steps of this process will be discussed and demonstrated, e.g.: (i) genome assembly or reassembly, (ii) gene finding/calling, (iii) manual proofreading of automatically generated sequences and predictions, (iv) comparative genomics, (v) consistent and biologically meaningful function assignment to genes and their products, (vi) phage lifestyle prediction, (vii) toxin finding, (viii) moron finding. Optional hands-on training and problem solving activities will be suggested.
Three major toolkits will be demonstrated in this section of the workshop:
- The SEED and RAST toolkits, including the latest development: RAST toolkit (RAST-tk), developed by an international team lead by the Argonne National Laboratory, IL, USA (http://www.theseed.org)
- PhAnToMe (Phage Annotation Tools and Methods) developed by the laboratory of R. Edwards at SDSU in collaboration with M. Breitbart and others (http://www.phantome.org)
- Tools recommended by A. Kropinski and maintained at: http://molbiol-tools.ca

RAST - http://rast.nmpdr.org
RASTtk - https://github.com/TheSEED/RASTtk-Distribution/releases/
MyRAST - http://blog.theseed.org/servers/installation/distribution-of-the-seed-server-packages.html
Prokka - http://www.vicbioinformatics.com/software.prokka.shtml
phAST - http://www.phantome.org/PhageSeed/Phage.cgi?page=phast
BASys - http://basys.ca/
GenSAS v3.0 - http://gensas.bioinfo.wsu.edu/
IGS - http://www.igs.umaryland.edu/research/bioinformatics/analysis/whole_genome.php
MWAS - http://www.yandell-lab.org/software/mwas.html

adapted from “Essential steps in characterizing bacteriophages: biology, taxonomy and genome analysis,” by Aziz RK, Ackermann H-W, Petty NK, and Kropinski AM.