Review Materials for Midterm1 of csc 487/687 Review for Midterm 1 It will be on October 13. Lectures 1-5 from the handouts are covered. Please refer to textbook, chapter 1, 3, and 4 (contents of chapter 4 before significance of alignments). Topics: Chapter 1: Introduction to bioinformatics The definition of bioinformatics field, its importance and major jobs What is nucleotide? The difference between RNA and DNA Nucleic acid chain and open reading frames (notice that there are several reading frames) The structure of DNA and RNA Genetic codes and how they work. The definitions of gene and genome. What is gene expression, and know how to describe the steps of gene expression. What is central dogma? Twenty amino acids of proteins. Structures of proteins (primary, secondary, tertiary, quaternary) Chapter 2 Computer Science Background for Biologists What is algorithm? Know how to design algorithms for a particular problem Know how to write pseudo-codes of algorithms when you design algorithms Know to analyze the time complexity or space complexity of a particular algorithm The meaning of NP-hard, NP-complete problems Chapter 3 Dynamic programming The meaning of dynamic programming The basic steps of dynamic programming The optimal structure of dynamic programming Know the applications of dynamic programming Chapter 4 Archives and Information retrieval Three primary public domain bioinformatics servers NCBI Entrez Nucleic acid sequence databases Public Protein databases How to use PDB and Rasmal Chapter 5: Sequence alignments The meaning of sequence alignments The difference between global alignment and local alignment. When global alignment or local alignment is an appropriate choice? The difference between pairwise and multiple alignment The meaning and applications of Dotplot The relationship between dotplot and alignments. Measures of sequence dissimilarity and sequence similarity. How to do sequence alignments using dynamic programming Different types of scoring matrices Substitution matrices and scoring matrices PAM and BLOSUM How to determine PAM The meaning of 1PAM, 2PAM… How to calculate Mz by matrix multiplication from M1 Log-Odds Scoring Matrix Gap penalty The types of problems in midterm include Term Explanation, True/False, short answers and some questions which maybe require the clear solution procedures. For example Term explanation Homologous sequences ― True/False Dayhoff makes use of the much larger amount of experimental data to build PAM scoring matrix than BLOSUM scoring matrix. False, because BLOSUM matrix makes use of the much larger amount of data that become available since Dayhoff’s work. If you think it is false, give a short explanation. Short Answer What is the major types of secondary structure in proteins? Some questions which maybe require the clear solution procedures. For example, ask you to design an algorithm to solve a particular problem, you should give the time complexity of your algorithm.
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