DNA Annotation & Bioinformatics

AUG

start codon or methionine

UAA, UAG, UGA

stop codon (do not code for any protein)

reading frame

triplet code requires translation to begin at the correct nucleotide

Shine–Dalgarno sequence

ensures that ribosome starts at the proper reading frame

Open reading frame (ORF)

AUG followed by a number of codons and a stop codon in the same reading frame

cluster

groups of phages that are organized based on genetic relatedness

GeneMark

program used to predict open reading frames (ORFs) and confirm that predicted ORF includes all of the predicted coding region

Phagesdb

database of all phages found by the SEA-PHAGES program

BLAST

basic local alignment search tool

looks for similarity between your phage’s ORFs and other previously identified sequences in a database

NCBI

The National Center for Biotechnology Information

HHPred

predicts the secondary structure of the protein and then selects matches with known structures

DNA Master

Compare your genome (or genes) to others in GeneBank using BLAST

starterator

allows visualization of the start site selections of all genes in a particular pham

phamerator

creates graphic maps to view nucleotide and amino acid similarity between phage genomes