Bioinformatics Exam 2 Study Guide

These flashcards cover key concepts and important details from the Bioinformatics Exam 2 lecture notes, focusing on topics such as sequence alignment, gene expression analysis, and biological networks.

What are the main materials covered in Bioinformatics Exam 2?

Domain analysis, gene expression analysis, structural bioinformatics, biological networks.

What percentage of the exam is dedicated to Structural Bioinformatics topics?

Approximately 40%.

What does MSA stand for in bioinformatics?

Multiple Sequence Alignment.

Which tool is commonly used for protein domain analysis?

Hidden Markov Model (HMM).

What is a significant application of Multiple Sequence Alignment?

It allows identification of conserved residues that are likely part of an active site.

What are RPKM and FPKM used for in RNA-seq data analysis?

They are methods for normalizing read counts based on gene length and sequencing depth.

What is the purpose of hierarchical clustering in gene expression data analysis?

To group genes or samples with similar expression patterns.

What type of analysis does a volcano plot provide in gene expression studies?

It visualizes statistical significance versus fold change of genes.

What defines a scale-free network?

A network characterized by a power-law degree distribution and the presence of hubs.

Which database is the major repository for 3D structural data of proteins?

The Protein Data Bank (PDB).

What is the principle of homology modeling?

It requires alignment of the target sequence to a known template structure.

True or False: RNA-seq has fewer advantages compared to DNA microarrays.

False.

What does the BioGRID database provide?

It includes over two million protein and genetic interactions.

What method can be used to determine if a Gene Ontology term is enriched in a gene list?

DAVID.

Why is normalization important in RNA-seq data analysis?

It ensures accuracy in comparing expression levels across samples.

In a co-expression network, what does each edge represent?

A significant co-expression relationship between two genes.

What analysis can be done using MEME software?

Discovery of DNA and protein sequence motifs.

How is a significant co-expression relationship identified between genes?

By observing similar expression patterns across various samples.

What does the abbreviation GO refer to in relation to gene lists?

Gene Ontology.

Which model is often used in gene expression clustering analysis?

Hierarchical clustering.

What does the mean path length in a biological network indicate?

It provides a measure of network connectivity.