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Day 1
Day 2
Day 3
Day 4
Day 5
Day 6
Day 7
Day 8
Day 9
Day 10

This page contains slides and supporting material for the Spring 2012 version of BMS270: Practical Bioinformatics without Programming. Please see the site updates page for archived versions and information on tracking changes.

General Resources

Safari Bookshelf

The Safari bookshelf provides on-line access to a large selection of computer books, primarily from O'Reilly. N.B.:

You need to be on the UCSF network to access Safari.
You need to authenticate your browser by visiting the main Safari Bookshelf link above before the book-specific links below will work.

The BLAST book

Excellent coverage of sequence alignment methods with an emphasis on BLAST. Of particular interest are the coverage of dynamic programming in chapter 3 and the protocols for common BLAST tasks in chapter 9.

Day 1: Sequence Similarity

Slides: Mark's slides for day 1
Entrez: NCBI Entrez cross-database search.
FASTA file format: Ad hoc FASTA specification from NCBI.
Feature Table Format: Specification for the feature table format shared by GenBank (.gb), EMBL, and DDBJ sequence files.
DOTTER: Dotplot sequence comparison program. Windows users should download windotter.zip from Eric Sonnhammer's page. OS X users should download pydotter.py instead. (Advanced OS X users may install DOTTER by installing GTK+ via fink and then downloading the OS X binary from AceDB page).
sequences1.zip: Example sequences for Monday's exercises.
Genes 167:GC1: The primary reference for DOTTER.

Fast, approximate dotplot tools

Pairwise BLAST: NCBI BLAST of two sequences includes a dotplot graphic
Ugene: Sequence "workbench" that includes a nucleotide dotplot tool
MUMmer: Very fast whole genome aligner

Day 2: Sequence Homology

Slides: Mark's slides for day 2
CLUSTALX: Multiple sequence alignment program based on neighbor-joining trees.
JALVIEW: Program for viewing and annotating multiple alignments. (The "Install Anywhere" version is slightly easier to install compared to the "Java Web Start" version).
GFF file format: Specification for the commonly used version 2 of GFF (e.g., this is what JALVIEW uses for sequence annotations).
GFFv3 file format: Recent update of GFF by Lincoln Stein, with stricter definitions and better support for relationships among features, as used by newer programs such as Gbrowse2.

Day 3: Heuristic Alignment and Searching

Slides: Mark's slides for day 3
NCBI BLAST: NCBI's BLAST portal
JMB 215:403: The primary reference for BLAST, giving a fast heuristic method for approximating the local alignment methods and a statistical framework for interpreting the results.
CABIOS 4:11: Myers and Miller's implementation of Smith-Waterman local alignment in O(MN) time and O(N) space. This is the pairwise local alignment method used by BLAST and CLUSTALW.
Web shuffler: A simple tool for shuffling sequences (to use as negative controls in, e.g. BLAST searches). You can also download a local version or view the source of the web version.
Cygwin: UNIX-like environment for Windows

Day 4: Multiple Alignment and Phylogeny

Slides: Mark's slides for day 4
CLUSTAL -> JALVIEW converter: Web tool to reformat bootstrapped CLUSTAL trees for JALVIEW

Day 5: Hidden Markov Models

Slides: Mark's slides for day 5
HMMer: Sean Eddy's profile-HMM implementation
HMMer web interface: New web interface to PHMMer, HMMscan, and HMMsearch
InterProScan: Search interface for InterPro, a meta-database of 15 motif databases (mostly HMM based)
PLoS Comp. Biol. 4:e1000069: Reference for HMMer 3 heuristic
Biological Sequence Analysis: In addition to excellent coverage of hidden Markov models (and the related dynamic programming algorithms for generating and searching with them) this book gives good general coverage of sequence alignment and statistics.
AGA1.fasta: Protein sequence of low-complexity mannoprotein from S. cerevisiae.

Days 6 and 7: Expression Profiling

Slides: Mark's slides for day 6
PNAS 95:14863 (Eisen et. al.): Paper introducing cluster analysis for microarrays.
supp2data.txt: Supplementary data for PNAS 95:14863 figure 2 (yeast expression profiles) converted to tab-delimited text (TDT) format.
better_shuffle.txt: supp2data.txt with rows shuffled to remove Eisen's gene clustering and headers modified for CDT format. Corrected annotations
fig1data.txt: Data for PNAS 95:14863 figure 1 (human fibroblast serum response) taken from the primary reference, Science 283:83
fig1data_shuffled.txt: fig1data.txt with rows shuffled to remove clustering
fig1data_shuffled_orderless.txt: fig1data.txt with rows shuffled and GORDER column stripped. (shuffling independent of fig1data_shuffled.txt)
Cluster3: Michael de Hoon's port of Michael Eisen's CLUSTER program.
JavaTreeView: Alok Saldanha's port of Michael Eisen's TREEVIEW program.
Numerical Recipes: Excellent reference for numerical methods. The older editions are available on-line at this link. The new (3rd) edition adds a chapter covering clustering and HMMs. See chapter 7.1 (and Comm. ACM 31:1192) for background on random number generators and chapters 14 and 15 for statistics and model fitting.

Day 8: Systematic Annotation and Graph Visualization

Slides: Mark's slides for day 8
Bioinformatics 20:3710: Primary reference for the SGD GO Term Finder
The Gene Ontology: GO Consortium homepage, featuring the AmiGO browser
GO Annotations: GO Consortium links to GO Annotated genomes
Evidence Codes: GO Consortium evidence code definitions
SGD GO Term Finder: Search for significant enrichment of GO terms in a set of S. cerevisiae genes (slow)
SGD GO Slim Mapper: Map a set of S. cerevisiae genes to a simplified GO subset, without statistics (fast)
SGD GO Tutorial: A guided tour of the GO resources at SGD
Cytoscape: Visualization/analysis tool for very large graphs. Supports pathways, interaction networks, gene ontologies, and expression data.
BiNGO: Cytoscape plugin for calculating enrichment of GO terms in a gene set (note that there are many tools for solving this problem, c.f., the GO consortium's list).
GraphViz: Command-line graph layout program from Bell Labs. Good for moderate-sized graphs. Inkscape is useful for exploring and annotating SVG output from GraphViz.
NetworkX: Python graph library from LLNL. Can connect to GraphViz and/or Matplotlib for visualization.
yeastHighQuality.sif: Yeast interactome graph from Cytoscape example directory
CellCycle_B.uids: Gene list from JavaTreeView for cluster B (cell cycle) from PNAS 95:14863
CellCycle_B.sif: Subgraph of yeastHighQuality.sif corresponding to the genes in CellCycle_B.uids

Day 9: 3D Structures

Slides: Mark's slides for day 9 (post-facto)
properties.pml: Example PyMol script
Colors.pml: Gianne's version of the example PyMol script. Mac users should try this one if properties.pml doesn't work.
RCSB/PDB: The protein databank
PyMol: Viewer for 3D protein structures (PDB files)
PyMol Introduction: Getting started tutorial
PyMol Commands: More in-depth command documentation
Selection Algebra: Wiki page on selection commands
RasMol: Older alternative to PyMol. Less pretty but nice for quick structure viewing.
1CLL: Calmodulin
2CHT: Chorismate mutase (B. subtillus)
1A02: Fos/Jun/NFAT with DNA (Nature 392:42)
1ASM: AATase
1QDM: Phytepsin (EMBO J. 18:3947)
1GID: P4-P6 Ribozyme
6TNA: tRNA

Day 10: Genome Browsing

Slides: Mark's slides for day 10
MochiView: Genome browser aimed at ChIP-chip, ChIP-seq, and motif finding. Download the full software (v1.45), the manual (pdf), the tutorial (pdf), and the tutorial database (cvw).
CGD: Candida albicans genome database (for the example data in the MochiView tutorial)
PLoS Biology 7:e1000133: Primary reference for the MochiView tutorial data set
sig_genes.mochiview: Sheet 1 of supplemental dataset S4 from PLoS Biology 7:e1000133 (giving control/zap1-/- log ratios for significantly differential genes) reformatted for MochiView
IGV: Integrative Genomics Viewer from the BROAD Institute. Similar to MochiView, but supports viewing aligned sequencing reads.
UGENE: Molecular biology "workbench" (similar to Vector-NTI) with support for viewing next-gen sequencing results (e.g., BAM files).
Motif finding tools: MEME is one of the first profile-based motif tools; it finds motifs in unaligned sequences using an EM algorithm. Monkey and RVista are more recent tools that use comparative genomics to reduce false positive signal.
Web of Science: UCSF links for the Web of Science and SCOPUS citation databases
PubMed RSS feeds: Tutorial on creating RSS feeds for PubMed searches
Ubuntu: Ubuntu Linux distribution. The installation CD can be booted as a "Live CD", allowing you to try Linux with no change to your computer.
Knoppix: Knoppix is a "Live CD" version of Debian GNU/Linux (the basis for Ubuntu). Knoppix may be a bit less user friendly than Ubuntu, but it may boot faster on some computers. More information about Knoppix can be found on this unofficial site.