Nucleotide Sequence Analysis 11:126:483 Syllabus
Week 1: Course introduction. Sequence file formats. Using DNAstar Lasergene EditSeq software. Importing and exporting sequence files in different formats. Manipulating DNA and protein sequences. Finding sequences in GenBank. Downloading sequences and importing into EditSeq. Importing GenBank sequences directly into EditSeq. Identifying research papers connected to a GenBank file. Searching for research papers in PubMed.
Week 2: Review of DNA sequencing with emphasis on automated sequencing. Design of a sequencing project. Preliminary inspection of data obtained from ABI automated sequencers. Looking for and eliminating vector sequences. Assembly of the final sequence. Inspection of the final sequence. Correcting errors.
Week 3: Review of restriction enzymes. Analysis of a sequence for restriction enzyme cutting sites. Use of a subset of the enzymes for the analysis. Looking for enzymes that do not cut, cut once, or cut twice. Design of subcloning experiments. Choice of cloning vectors to match the fragment to be cloned. Review of translation (normal and alternate starts and stops, ribosome binding sites, etc.) Finding open reading frames. Alternate codon tables. Codon usage analysis. Translating the DNA sequence to a protein sequence file.
Week 4: Practice exams.
Week 5: Practical exam
Week 6: Accessing publicly available databases on the internet (NCBI). Searching for a sequence by name. Blast searches: identifying genes and proteins. Differences between nucleotide and amino acid sequence searching. Searching for related sequences.
Week 7: Searching for and downloading batches of sequences. Aligning sequences. Determining sequence relatedness. Drawing dendrograms.
Week 8: Genomic and motif analyses. Amino acid sequence analysis.
Week 9: Practice exams
Week 10: Practical exam
Week 11: Independent sequence analysis projects.
Week 12: Independent sequence analysis projects.
Week 13: Independent sequence analysis projects.
Grading: 30% each exam, 30% final project, 10% attendance and assignments.
Exams: The two exams will include a combination of sequence analysis and problem sets using the computer programs that we have used in class. There will be a limited amount of time for each exam so the better you know the software programs the more likely you will complete all of the problems on the exam.