review_midterm by keralaguest

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									          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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