Training Materials
Training Content
- Overview of Genome Basics
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How to find where genes are located on the genome.
- Finding closest relatives
- Compare your genome to those of closest relatives
- How are the locations of genes predicted
- How do you add and delete genes
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How do you find the correct start site for a protein coding gene
- Gaps
- Ribosomal binding site metrics
- Coding Capacity
- ORF (Open Reading Frame)
- Weighing all of the Evidence
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How do you find the correct start and stop site for a tRNA or a tmRNA gene
- tRNA Gene
- tmRNA Gene
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How do you annotate translational frameshifts
- Tail assembly chaperone protein genes
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How do you find the function of a protein coding gene?
- PhagesDB
- HHPred
- NCBI BLAST
- Conserved Domain Database
- Transmembrane predictions
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How do you annotate or quality check the function & synteny of a protein coding gene
- Function
- Synteny
- Notes, final review, and quality checking
PECAAN Video Tutorials
Overview and Genome Basics
Introduction to phage genomes and basic annotation concepts.
Finding closest relatives
Learn how to identify evolutionary relatives of your phage.
Compare genome to closest relatives
Comparative analysis techniques for genome annotation.
How the locations of genes are predicted
Understanding gene prediction algorithms and tools.
How to add and delete genes
Practical guide to modifying gene annotations in PECAAN.
SEA PHAGES annotation guide
Comprehensive guide following SEA PHAGES standards.
Starterator, PhagesDB & NCBI BLAST
Using external tools for start site determination.
Gaps & Ribosomal Binding Sites
Analyzing intergenic regions and RBS sequences.
GM coding capacity, LORF & start sites
Advanced techniques for start site selection.
tRNA and tmRNA
Annotating transfer RNA and transfer-messenger RNA genes.
Assigning a function
Methods for determining protein function and annotation.