BME150, Spring 2012, Section 01: Computational Biology Workshop

Pre-workshop:

1. Download Jalview

·      -Go to Jalview website (here) and click "Install with InstallAnywhere"

·      -Jalview is a multiple sequence alignment editor

2. Locate a text editor

Word has hidden formatting that you don't see in files.  Computational biology programs need plain text files and can't process word files.  Please locate these text editing programs or download one of the suggested programs. 

·     -For Mac, find TextEdit

·      -For PC, find Notepad

·      -Optional: Download one of these fancy text editors.  These text editors have more capability such as tabs, line numbers, and column selection.

Editor Supported Platforms
Notepad++  Windows
Jedit  Windows, Mac
TextWrangler  Mac  

Starters

Entry forms for questions generated from starters

Form for Starter 1 questions (Mia)

Form for Starter 2 questions (Paola)

Form for Starter 3 questions (Lauren)

Pictures of Phylogenetic trees

Tree of Life

Vertebrates

Mammals

Mammals: Platypus, Rat, Human, Mouse, Cow, Dog, Horse

Archaea

Mia's starter

See files in the "Attachment" section below.

FOXP2_Seqs.fasta

FOXP2_Seqs_2.fasta

Lauren's starter

Lauren's worksheet

Blast-L7ae.fasta

Focused Investigation

Template for taking notes

This is a template for taking notes during your focused investigation. Directions on what to write in it and how to share it are inside.

Template 

How to take screenshots to save in your Google document

For Mac:

1. Set up the screen so that what you want to shoot is in front of other palettes, images and programs. What you want to shoot a screen of can be anywhere on your screen(s).

2. Press the Command+Shift+4 buttons on the keyboard. This will initiate the capture mode.

  • Clicking on the screen will take a capture of the entire screen.
  • Clicking and dragging a marquee will take a screen of everything within the marquee.
3. Your image will be on the desktop. In your Google document, click on the insert image button (Looks like a grey square with white mountains in it) and drag the picture into the document.


For PC: (from BetterPhoto)

Screen shots on a PC can be taken without a special screen shot utility using the built-in Print Screen function. You can take a shot of the entire screen, or use the ALT key to confine the screen shot to the fore-most window (may be a program window or dialog/alert). Using Print Screen will capture the content of the current screen in the clipboard. Paste this image into your google docs

Here are the steps:

1. Set up the screen so that what you want to shoot is in front of other palettes, images and programs. Be sure the palette/window is over the program window (for example, a palette can be detached from the palette well, but it should not be on a second monitor if you have a two monitor setup).

2. Press the Print Screen button on the keyboard. This will capture the screen and place it on the clipboard. Hold down the ALT key before pressing the Print Screen button to confine the screen shot to the foremost window.

 Day 2

Groups for documentation exercise below.  

Importance of Documentation

Tuesday

Ben Morck Kevin Lam  
Jessica Ruby David Oda  
Jacob Schreiber Jackson Burnette   
David Swartout Michael Alonge  
Allison D’Souza Kevin Lai  
Wilson Liu Greta Hull  
Ranna Khorram  Andrew Prokop  
Logan Mulroney John Vivian  Lisa Nguyen 



Wednesday

William Paulson Chethan Jujjavarapu  
Subrina Bhuiyan Boris Brenerman  
Cameron Pernia Peter Maguire  
Paul LeDuff Divya Sharma  
Chad Townsend Abigail Munoz  
Warren Cotten John Collins Jose Morales
Kiku Koyano Matthew Prout  
Kyle Langan Rahul Parulkar  
Sidhand Karamchandani Aaron Fojas  

Workshop Survey

Survey Link

 

Homework 

1. With your group pick a interesting result or phenomena that you observed during your focused investigation, in particular using a computational biology tool.  Write directions so that another group can reproduce what you did.  It should take the other group about 5 minutes to reproduce.

2. Complete worksheet on E-values and P-values (below).  We recommend trying to fill out the sheet before you read the handout as an exercise to see what you know.

Computational Biology Tools:

Translate DNA to Protein, and more!

This program can reverse, complement, and translate a sequence: Translate

Genome Browsers

UCSC Genome Browser For eukaryotes, including human, fly, yeast, and mouse
UCSC Microbial Genome Browser For bacteria and archaea

BLAST

 

BLAST: Basic Local Alignment Search Tool

    -Use to search for protein or nucleotide sequences similar to yours

Flavors of BLAST:

blastn - search a nucleotide database using a nucleotide query

blastp - search protein database using a protein query

blastx - search a protein database with a nucleotide query that is translated

tblastn - search translated nucleotide database with a protein query

tblastx - search translated nucleotide database with a nucleotide query that is translated 

Databases

 

NCBI National Center for Biotechnology Information Home of Genbank, Pubmed
Pfam Protein Family Database

Collection of protein families, represented by multiple sequence alignments and Hidden Markov Models

PDB Protein Data Bank 3D structures of proteins
OMIM Online Mendelian Inheritance of Man Database of human genes and genetic disorders
COSMIC Catalog of Somatic Mutations in Cancer  

Mutation impact predictors

MutPred Classifies an amino acid substitution as disease-associated or neutral in human
SIFT Predicts whether an amino acid substitution affects protein function based on sequence homology and the physical properties of amino acids
PolyPhen Predicts possible impact of an amino acid substitution on the structure and function of a human protein using straightforward physical and comparative considerations

Multiple Sequence Alignment

MAFFT Available in Jalview 
MUSCLE Available in Jalview 
CLUSTALW2 Available in Jalview 
T-COFFEE  

Attachments