ELab Report 1: Genomics and Bioinformatics Review

Vocabulary review covering genomic assembly terminology, BLAST parameters, homology types, MEGA12 software symbols, and phylogenetic tree characteristics.

Coverage

The number of times a DNA base has been sequenced; it is an important measure of quality.

De novo assembly

A method to piece together the genome from reads without using a reference genome; it is unbiased and identifies structural rearrangements.

Contig

Each length of assembled sequence.

Closed genome

A genome assembly consisting of a single contig.

Draft genome

Several contigs separated by gaps for which we do not know the sequence.

BLAST (Basic Local Alignment Search Tool)

A tool that finds regions of similarity between a sequence and a database.

Galaxy

Software used to annotate contigs for you.

Short read data limitations

Technology using reads of $150\,bp$ struggles with repetitive or duplicated regions longer than $150\,bp$, resulting in multiple contigs instead of a closed genome.

Reference-based assembly

An assembly method ideal for highly related genomes that allows more of the genome to assemble, though it may be biased and struggle with novel sequences.

ORF (Open Reading Frame)

Any stretch of DNA beginning with a start codon and ending with a stop codon in the same translational frame.

Max Score (BLAST)

The highest alignment score out of all aligned segments from the database.

Total Score (BLAST)

The total score of all aligned segments.

Query Cover (BLAST)

The percentage ($\%$) of your searched sequence which is matched by the database sequence.

E Value (BLAST)

The expect value; a statistical measure of significance representing the number of hits expected purely by chance. A lower value suggests high significance.

Ident (BLAST)

The percentage ($\%$) amino acid identity of the query sequence to the database sequence.

Accession

A unique identifier for a sequence in a database.

Homologue

Two genes which evolved from a single ancestral gene.

Orthologues

Homologues which have arisen only from genome replication and speciation.

Paralogues

Homologues which have arisen from gene duplication within a genome.

Alignment

The process of comparing two sequences presumed to have a common ancestor/function and lining up residues to find differences.

Phylogeny

The practice of taking alignment information to construct a phylogenetic tree to study the evolution of nucleotide sequence or function.

SNP (Snips)

Single Nucleotide Polymorphism; a 1-letter change in genetic code that must occur in at least $1\%$ of the population.

Indel

A mutation involving the insertion or deletion of one or more nucleotides, often indicated by gaps or ($---$) in alignment sequences.

A256T

An example of annotating an SNP where "A" is the nucleotide before, "256" is the base position, and "T" is the nucleotide after.

Asterisk ($*$)

The symbol used in a translated amino acid sequence in MEGA12 to mark a stop codon.

Question mark ($?$)

In amino acid sequences, this indicates a codon is split across two sides of an indel.

Bootstrapping

A statistical method used in trees to show the confidence level by indicating how many times the system relates two things.

Scale bar (Phylogeny)

An indicator of the amount of genetic change or evolutionary divergence represented by horizontal branch lengths.

Core Genome

The set of genes present in the vast majority of genomes ($>90-95\%$).

Accessory Genome

The set of genes which are present in some genomes but not others.

Pangenome

The combined core and accessory genome; the complete set of all genes in a set organism.

FASTA Format

A compressed file format used for concatenated core aligned sequences.

Lecithinase and lipase egg yolk agar profile

The phenotypic method suggested to differentiate between C. botulinum and C. butyricum.

Multiplex PCR

The molecular method suggested to differentiate between C. botulinum and C. butyricum.

Whole genome sequencing (cgMLST or SNP analysis)

The sequencing-based method suggested for OzFoodNet to differentiate between C. botulinum and C. butyricum.