Outline for BIO 325 Bioinformatics - Fornari (spring semester 2006)

Review, Part I, II, III, IV, V, VI Resources Page


Review

Chap.

Topics and CRAaP

NCBI text-
books;
library texts
Central Dogma,
Molecular Biology Primer; Sequence Properties of Nucleic Acids & Proteins;
NCBI Literature Databases (BookShelf).
HA text: ch.2: p.12-25 only (no PCA)
KR text: ch. 1 all (excellent review)
Handouts
(HO's)		 Genetic Code; IUPAC letter codes for nucleotides and amino acids
 
 

 

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Part I: Sequence Databases and Information Retrieval

Chap.

Topics and CRAaP

3VBub

 VBub text: ch. 3: p.45-61 (the databases);
BO text: chs. 1 & 3 (DB's and accessing them - see entries below)
Accessing Molecular Genetic Information through the Internet:
the NAR Molecular Database Collection 2008 Update;
NAR Database Issue
NAR WebServer Issue
NCBI's Entrez
1BO

 BO text: ch. 2: p.15-26: Nucleotide Sequence Databases; GenBank, EMBL, DDBJ, all as part of INSDC; accession numbers & annotations - a perspective
VBub text: ch. 2: p.15-26: Protein Sequence Databases; UniProt

3BO

BO text: p. 56-70: NCBI's Entrez, especially figures 3-11 to 3-15; p. 74-77: OMIM, the grandest Medical Database

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Part II: Pairwise Sequence Comparisons

Chap.

Topics and CRAaP

4VBub

text, p. 41-50: some definitions, biology of homology
text, p. 50-62: PAM & BLOSSUM scoring matrices
text, p.62-73: global & local alignment algorithms
text, p.73-79: statisical significance of pairwise alignments


 11BO

 BO text, p. 296-298: Dot Plots (Dotlet Program)
BO text, p. 298-304: Scoring Matrices
BO text, p. 304-311: Introduction to BLAST
BO text, p. 311-314: BLAST Options
 

Article: "Gene Families - The Taxonomy of Protein Paralogs and Chimeras" by S. Henikoff, Greene, Pietrokovski, Bork, Atwood, and Leroy Hood
p. 323 of BO text for Problem Set: 1 and 2 parts a-e

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Part III: BLAST, FASTA, and Advanced BLAST

Chap.

Topic

4-5JP

JP text, p. 100-108: theory - how it works and evaluating results
Biostatistics-Statistics Software Programs Betty C. Jung's
JP text, p. 87-100: practice - using BLAST effectively
JP text, p. 108-114: searching strategies
JP text, p. 127-135: specialized BLAST sites
Project Ensembl and TIGR
JP text, p. 137-144: PSI-BLAST theory and practice
JP text, p. 147-151: Using BLAST for gene discovery

11BO

BO text p. 315-320: FASTA, especially figs 11.19 and 11.20
BO text, p. 304-311: BLAST theory, especially figs. 11.7 and 11.8
BO text, p. 311-312: BLAST 2 Sequences
BO text, p. 312-314: PSI-BLAST, especially fig 11.15

 

Articles: "Having a BLAST with bioinformatics (and avoiding BLASTphemy)"
by A. Pertsemlidis and J.W. Fondon III
and "How 90,000 lines of code helped spark the Bioinformatics explosion"
by Anne Harding

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Part IV: Protein Sequene and Structure Analyses

Chap.

Topic

8JP

JP text, p. 223-246: 4 essential perspectives on proteins: (1) domains and motifs, (2) physicla properties, (3) protein localization, (4) protein function.
See: Gene Ontology for these perspectives in action,
and GOA at EBI
JP text, p. 247-267: proteomics; methods, practices, databases

9JP

JP text, p. 273-276: introduction to protein structure and structural genomics
JP text, p. 276-283: principles of protein structure & protein folding
JP text, p.287: X-ray crystallography and NMR (handouts)
JP text, p. 287-303: the PDB, RCSB, SCOP, CATH, DALI, FSSP & others
JP text, p.303-313: Computational approaches and visualization, see especially UCSF Chimera and MultiAlign

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Part V: MSAs or Multiple Sequence Alignments

Chap.

Topics and CRaP

10JP

JP text, p.319-325: Introduction to MSAs and the Feng-Doolittle algorithm
JP text, p.325-329: Hidden Markov Models, theory (handouts & lecture) and practice; see: Hidden Markov Models and Hidden Markov Model-2
and a web-based server for HMM build, calibrate, and search
JP text, p.341-346: User-generated MSA alignments; see ClustalW at EBI, and MUSCLE and MAFFT Fast Multiple Sequence Alignment and FlowerPower
JP text, p.331-341: databases of MSAs; Pfam, SMART, CDD, BLOCKS, PopSet, and more...
See the CEMC server for Multiple Protein Structure Alignment
at the Center for Excellence in Cancer Genomics

ann_rep1 frags.fa
12BO

p. 326-327: What are MSAs?
p. 327-330: Hierarchical and non-hierarchical Methods
p. 330-331: MSAs by PSI-BLAST
p. 332-336: Tools for MSAs

3D-PSSM Protein Fold Recognition (Threading) Server

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Part VI: Molecular Phylogenetic Analyses

Chap.

Topics and CRAaP

11JP

p. 357-365: Introduction to Molecular Evolution, the Molecular Clock Hypothesis, and Neutral Evolution
p.365-370: Tree nomenclature and structure;
p.370-379: the 4 stages of Phylogenetic Analysis
p.383-386: tree-building methods, NJ, MP, ML
p.386-389: tree-evaluation methods, the Bootstrap

PhyML: simple, fast accurate algorithm for ML

14BO p.366-368: Why Phylogenetics? Introduction to the basics
p. 368-373: Models, Assumptions, & Interpretations
p. 373-383: How to construct a Tree in 4 steps; the differences
between Parsimony, Distance, and Likelihood algorithms
(Beware of UPGMA!) and What about Bayesian algorithms??
p. 384-388: PHYLIP, PAUP*, & other software
 

PAUP - on computers in rooms 205, 219, 223; we are now using MEGA 3.1

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