Genomics and Metagenomics
The step that involves putting small DNA pieces together into larger sequences computationally is called this.
(Genome) Assembly
In Proteomics PAGE stands for
Polyacrylamide gel electrophoresis
This marker gene is commonly used to evaluate prokaryotic microbomes
16S rRNA gene
This command is used to determine your working directory
getwd()
We used this computer program to build alignments from sequencing data
MEGA
These are subsequences of length k derived from a DNA or RNA sequence, often used in genome assembly and sequence analysis.
kmers
This type of sequencing is used to measure gene expression levels by sequencing the RNA in a sample.
RNA-seq
ASV stands for this
Amplicon Sequence Variant
We used this R library to visualize our data
ggplot or ggplot2
This type of alignment arranges DNA, RNA, or protein sequences so that homologous positions line up for comparison.
Multiple Sequence Alignment
MAGs stand for
Metagenome assembled Genomes
In transcriptomics, this process converts RNA into complementary DNA before sequencing, because most sequencing platforms cannot read RNA directl
Reverse transcription
A distance metric that is commonly used to quantify beta diversity, measuring how different microbial communities are from one another.
Bray-Curits
Unifrac
Euclidean
The four windows that make up R studio are:
Source (Script editor) on top left, Console on bottom left, environments (top right), output (bottom right)
This component of a phylogenetic tree represents a lineage, a group that originates from a common ancestor.
What is a branch
During metagenomic binning, these characteristics of sequencing data are used to group sequences from the same genome (Name2)
GC content
Tetranucleotide frequency
Differential Coverage
Marker genes
During a Western Blot, these small molecules are used to specifically detect the presence of a protein of interest in a sample.
Antibodies
These hierarchical levels are assigned to sequences during taxonomic classification in amplicon analysis
phylum, class, order, family, genus, and species
This vegan function is commonly used to calculate ecological distances, such as Bray-Curtis, before performing ordination analyses.
vegdist()
This tree-building method constructs phylogenies by first generating a distance matrix from alignment data and then clustering taxa based on pairwise distances.
Neighbour joining
UPGMA
During functional annotation, gene prediction tools commonly follow these steps
1) Identify Open Reading Frame (ORFs)
2) Translate ORFs to protein sequences
3) Compare predicted proteins to reference databases
4) Assign function/pathways
Comparing upregulated and downregulated genes under different conditions is part of this type of analysis.
Differentional Expression analysis
This diversity metric incorporates both richness and evenness and is commonly used to compare community complexity between samples.
Shannon diversity index
In R, converting wide/tabular data to long format for easier plotting or analysis is commonly done using the _____ library and the _____ function.
tidyr/tidyverse library and pivot_longer() function
These are genes in different species that evolved from a common ancestor and retain the same function
orthologs or orthologous genes