Mary Shaw - New Mexico Highlands University

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January 9, 2007


Biology 435/535 ST:Research Exploration in Genomics

Spring 2007

2 credits, 1 lecture hour and 2 laboratory hours

Lecture/Discussion T10-10:50, Lab R 10-11:50 AM

Biology 692 Independent research

last taught Fall 2010

2 credits


Dr. Mary Shaw, Life Science Department, Office: HSCI 325

Phone 454-3407; e-mail

Office Hours: M, W 11-11:50 and M, W 2-3:30, or by appointment


This course is part of the Genomics Education Partnership at Washington University in St. Louis, MO. In this course students will analyze and annotate a fosmid containing DNA from the dot chromosome of a Drosophila sp. that has been sequenced by the Washington University Genome Sequencing Center. The information will be contributed to the publication on the sequencing and annotation of the entire chromosome.


No text book is required. The following books maybe useful.

  • Bioinformatics and Functional Genomics, R. Pevsner, 2003 J. Wiley and Sons
  • Exploring Genomes: Web-based Bioinformatics Tutorials, Raul G. Young, 2003 Freeman & Co.
  • BLAST I. Korf, M. Yandell, and J. Bedell, 2003
  • Genomes 2, Terrance Brown, 2002 Wiley-Liss


At the completion of the course students will be able to analyze and annotate genomic sequence data using commonly used DNA data bases such as:

  1. model organism websites
  2. genome browsers
  3. RepeatMasker
  4. Genscan and other search tools
  5. BLAST and BLAT searches for similarity
  6. Clustal for comparative analysis


The course will consist mainly of laboratory work to evaluate and annotate a particular fosmid sequence. Attendance is required and make-up sessions are not possible. If you must miss a class please inform Dr. Shaw PRIOR TO THE CLASS SESSION. If you miss class YOU are responsible for obtaining any notes, announcements or other information from your lab partner, the TA or Dr. Shaw. Assignments will be accepted up to 1 week late with penalty of 20%. After one week they will not be accepted due to any circumstances. All students will be required to submit a brief written paper review. Graduate students will present and explain the paper to the class in addition.

Independent study students will be assigned a fosmid and we will consult on an as need basis depending on the experience of the student


Paper review and/or presentation: 15%

Problem sets: 25%

Written report on fosmid analysis and annotation: 35%

Presentation on fosmid analysis and annotation: 25%


  1. I will not speak when others are speaking.
  2. No cell phones are allowed in class. If you are expecting an important call please put the phone on "stun".
  3. Each student is responsible for his or her own work on each assignment, although collaborations and discussion during preparation are encouraged.
  4. As members of a scholarly community dedicated to healthy intellectual development, students and faculty are expected to share the responsibility for maintaining high standards of honesty and integrity in their academic work. Each student should reflect this sense of responsibility toward the community by completing and submitting work that is a product of his or her own effort in a particular course, unless the instructor has directed otherwise. All instances of academic dishonesty will be reported to the dean.
  5. All class participants are expected to conduct themselves in a professional manner.
  6. Students needing disability assistance should contact student services at 454 3252.