A collection of 12 online bioinformatics lectures and exercises. The topics include: Working with UNIX, Finding Sequences in Databases, Similarity searching, Pairwise and Multiple Alignments, Sequence-Function Relationships, Phylogenetics, SeqWeb and SeqLab: Graphical Interfaces for bioinformatics, Computer Tools for Sequencing Projects, PCR and Restriction Mapping, Genomics, The Internet for Biologists. The site has the lecture notes for the course as both web pages and as Powerpoint slides, along with weekly assignments for the students. The lecture notes have detailed instructions for how to use a UNIX system, including instructions on editing with EMACS, using ftp, printing, etc. The primary bioinformatics suite that is used for this course is GCG version 10, but there is also extensive coverage of the use of free online web sites such as ENTREZ and email sites. These is also some coverage of the graphical SeqLab user interface for GCG. For searching the course describes the uses of FASTA, BLAST and Smith-Waterman programs such as SSEARCH or BLITZ. For multiple alignments only the GCG program PILEUP is covered in any detail, though CLUSTALW is mentioned. The chapter on functional analysis covers promoter finding, ORFs, RNA folding and protein structure. The phylogenetics chapter is brief and while giving some basic background, does not go over the usage of programs such as PAUP or the PHYLIP collection in the same detail as the earlier chapters. Fragment assembly, restriction mapping, PCR primer design, and genomics also get brief treatments.
Type of Material:
Lecture notes and online assignments
Recommended Uses:
Could be used as an entire course in bioinformatics. Single lectures or exercises could also be modified for an individual course.
Technical Requirements:
Some of the exercises use UNIX based programs.
Identify Major Learning Goals:
Learn the basic principles of bioinformatic analysis of DNA, RNA and protein sequences.
Learn how to use the GCG suite of programs on a UNIX computer
Learn to use some common web-based tools for sequence analysis
Target Student Population:
Upper level undergraduate or graduate student.
Prerequisite Knowledge or Skills:
Strong molecular biology background
Content Quality
Rating:
Strengths:
Good explanations of the underlying processes for each type of analysis of many bioinformatic programs and how to use them
Concerns:
Many of the later chapters are incomplete with not enough detail on how the programs work or can be used
More recent bioinformatic topics such as microarray analysis, whole genome comparisons, etc. are not discussed
Many of the web links are broken
GCG is not being developed anymore, so discussion of substitutes such as EMBOSS would be helpful
Potential Effectiveness as a Teaching Tool
Rating:
Strengths:
There are many useful tutorial type exercises
Effective use of graphics and very clear descriptions
The "Web motif and function" assignment is open-ended and challenges the student to go beyond the analysis described in the lecture notes
Concerns:
Not enough exercises like the
"Web motif and function" assignment
Out-dated programs and the focus on the no longer developed GCG program limit the applicability of the instruction
Ease of Use for Both Students and Faculty
Rating:
Strengths:
Easy to navigate, runs smoothly, well organized outline.
Concerns:
Too many broken links
Requires use of UNIX based programs that may not be available on most campuses.
Creative Commons:
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