Instructors: Guo-Liang Wang and Eric Stockinger

Click below to download handouts and reference papers as PDF files

One slides/page lecture notes

Four slides/page lecture notes

Reference paper 1

Reference paper 2

Course video

Printed copies of handouts will not be provided in class. Please print out your own handouts.

Study questions

1. Define genotype and phenotype and explain the relationship between them. Define what a gene is in pre-genomics classical Mendelian thinking terms and in post-genomics modern era terms. What is the difference between locus and allele?
2. List four different strategies that can be used to physically identify the gene underlying a phenotypic trait (from the perspective of a geneticist or a biologist). List three approaches to bioinformatically predict genes from DNA sequence.
3. In aligning sequences what is the difference between a local alignment and a global alignment? What is the difference between pair-wise sequence alignment and multiple sequence alignment? What types of alignments does BLAST do? What is a query sequence and what is a database sequence? What is an E-value? Which is the more significant match to a query sequence, a hit with a low E-value and high score, or a hit with a low score and high e-value? Why? BLASTN compares a query sequence to a nucleotide database while BLASTX translates that same query sequence into six protein sequences and compares it to a protein database. Which is usually more informative in finding protein-encoding genes? Why.
4. What is a start codon? What is a stop codon? What is an open reading frame? How many different reading frames are there in a fragment of DNA? What does the term codon usage describe? What are some of the other gene features used to train computer programs to predict genes from prokaryotic genomic DNA sequences? What additional features does eukaryotic genomic DNA have that are useful in training computer programs to recognize genes? How can one check whether the computer program accurately predicted a gene?
5. How might aligning large segments of genomic DNA (100 – 200 kb) from two different organisms help find genes? How does a dot plot visually aid in finding regions of nucleotide identity between two genomic segments? If you compare a sequence to itself (along the x and y axis), what line configuration will be obtained in a dot plot? If your sequence has a series of direct repeats on it, what additional features are expected? What line configuration would an indirect repeat produce?