Mini-assignment #4 Resources

Papers

The Bacterial Species Challenge: Making Sense of Genetic and Ecological Diversity

Functional Classification Using Phylogenomic Inference

Metagenomics: A Call for Bringing a New Science into the Classroom (While It’s Still New)

Do orthologous gene phylogenies really support tree-thinking?

Supporting Online Material for The Tree-Thinking Challenge

Phylogenies & Tree-Thinking

Understanding Evolutionary Trees

Web Resources

National Center for Biotechnology Information
http://www.ncbi.nlm.nih.gov/

ExPASy Proteomics tools
http://www.expasy.org/tools/

The Biology WorkBench is a web-based tool for biologists. The WorkBench allows biologists to search many popular protein and nucleic acid sequence databases. Database searching is integrated with access to a wide variety of analysis and modeling tools, all within a point and click interface that eliminates file format compatibility problems.
http://workbench.sdsc.edu/

Resource for Studying Biological Macromolecules: Protein Data Bank
http://www.rcsb.org/pdb/home/home.do

The ConSurf Server
Server for the Identification of Functional Regions in Proteins
http://consurf.tau.ac.il/

BioQUEST Curriculum Consortium
Community Resources for Problem Solving in Biology
http://bioquest.org

Where Are We? Evolution Survey
http://bioquest.org/blog/2009/02/waw-evolution/

BEDROCK

Whippo Problem Space
http://bioquest.org/bedrock/problem_spaces/whippo/

Participant Projects
http://bioquest.org/bedrock/participant_projects.php

ESTEEM

EvolSeq
This worksheet simulates the molecular evolution of DNA sequences. The program begins with a single (random) sequence, then follows that sequence through time as it reproduces and mutates. Eventually, up to 20 evolutionary related sequences are generated. EvolSeq then calculates the genetic distances between each pair of DNA sequences, and also between the associated amino acid sequences.
http://bioquest.org/esteem/esteem_de...product_id=194

Split Decomp
This worksheet performs split decomposition on a set of four DNA sequences and their associated amino acid sequences. The user can type in the sequences or paste them in from a text file. The program then translates the DNA sequences into amino acid sequences and calculates split indices and four-point conditions for each of the three possible unrooted phylogenies. The user can use these values to assess the data support for each of these topologies.
http://bioquest.org/esteem/esteem_de...product_id=195