Similar to the lecture notes on Repetitious DNA, this is a PowerPoint presentation given by Dr. Jeremy Buhler for the GEP faculty and TA workshops. This presentation covers the basics of RepeatMasker, as well as limitations of the program that students should be aware of.
This lecture uses the themes from Slide Sets 1-3, of the “F Element Project: Annotated Lecture Slides” sequence, in describing what we have learned about the F element—combining wet-bench work in the Elgin lab, results of chromatin mapping by the modENCODE consortium, and the bioinformatics efforts of the faculty and students of the GEP. This includes the following:
This lecture introduces students to the analysis of repetitious elements in the genome. It can be used as a stand-alone lecture, or since the content is also important to our thinking about the relationship of transposable elements to eukaryotic genomes which is a key issue in our study of the expanded F element, it can be included in the “F Element Project: Annotated Lecture Slides” sequence.
The slides provide each of the following:
Without our TEs and histones, we would be bacteria!
This lecture develops the relationship between chromatin packaging and control of gene expression, a significant epigenetic system that allows the genome to respond to changes in environment, both the external environment and physiological cues (e.g., hormone responses). There are 7 slides developing the importance of epigenetic regulation, particularly the silencing of repeats by heterochromatin packaging; 6 slides on histone post-translational modification; 9 slides on the discovery of Heterochromatin Protein 1a and its validation using Position Effect Variegation (in Drosophila), including the model for spreading of heterochromatin; 8 slides on HOW heterochromatin packaging can lead to silencing; 3 slides on the inheritance and manipulation of the heterochromatic state; and 4 slides on mapping chromatin states across the fly genome.
This video provides a 50-minute talk on our motivation and progress for the F Element “expansion” Project. The talk briefly introduces the
The slide set used in the video is provided as a PowerPoint (automatic download) and a PDF Handout using the buttons below.
Notes from a lecture on sequence alignment given by Dr. Jeremy Buhler in the Bio 4342 course at WU. The lecture covers the theory behind BLAST as well as some of the potential problems and limitations of BLAST.
Similar to the Lecture Notes on Alignment, this is a PowerPoint presentation given by Dr. Jeremy Buhler for the GEP faculty and TA workshops. This presentation covers the basics of alignment, essential for students to correctly interpret BLAST results.
This exercise continues your introduction to practical issues in comparative annotation. You will be annotating genomic sequence from the dot chromosome of Drosophila mojavensis using your knowledge of BLAST and some improved visualization tools. You will also consider how best to integrate information from high-throughput sequencing of expressed RNA.
An introductory exercise using BLAST to annotate a region in the Drosophila melanogaster genome. Students can use this exercise to gain familiarity with performing BLAST searches and interpreting BLAST output. An answer key is provided for instructors.
