Bioinformatics Computing: Articles and Resources

• Class Handouts
• Chapters 1 & 2: Genes
• Chapters 1 - 4: Genes
• Chapters 5 & 6: RNA and Protein Synthesis
• Chapter 2: Pairwise Alignment
• Prediction of Complete Gene Structures in Human Genomic DNA
• Blast
• Blast_article.pdf
• Article Figures
• BioinformaticMilestones.jpg
• Scalablast
• Sequencing
• SequencingArticle.pdf
• Article Figures
• SequencingMilestones.jpg
• Fundamental Algorithms in Sequence Analysis (ppt)
• Gene animations (here)
• Stochastic Context Free Grammars For tRNA Modeling (pdf)
• Bioinformatics—An Introduction for Computer Scientists (pdf)
• Biological Animation
• Article (The Scientist)
• Example (Nature) flash format; mov and avi formats also available
• Podcasts
• Genomes of Parasites (Science Friday, NPR), mp3 format; click to play (if your browser supports mp3) or right click to download and then load into your rmp3/iPod player
• SciFri Podcast - 2005071512 - Parasite Genomes 21:37 7/18/05 The genomes of several parasites responsible for diseases have been sequenced. We'll talk about the work and whether it could lead to cures for sleeping sickness, Chagas disease and leishmaniasis.
• Articles on Transposons
• Molecular evolutionary analysis of the widespread piggyBac transposon family and related ''domesticated'' sequences
• Tsessebe, Topi and Tiang: three distinct Tc1-like transposable elements in the malaria vector, Anopheles gambiae
• P elements are found in the genomes of nematoceran insects of the genus Anopheles
• HMM Tutorial
• Premier Courseware of 2005
  
  Late October 2005, the Premier Courseware of 2005 were announced at the 2005 Frontiers in Education conference. One winner was:
  
  Biological Information Handling: Essentials for Engineers By Mary Lidstrom, Cate Speake, David Farkas, Alicia Ann McBride, Patricia Kirkham and Quan Zhou of the University of Washington, and Marc Hoffman and Bob Lindenmayer of Poison Dart Frog Media. Biological Information Handling: Essentials for Engineers enables engineering students to acquire the language and understand the most fundamental of all biological processes, those involved in information transfer of the cell (replication, transcription, and translation). The Biological Information Handling is a self-paced, interactive independent study tutorial that teaches the fundamentals of information transfer in biology to engineers from an engineering perspective. It has been used as a curricular supplement to introductory bioengineering courses in chemical, electrical and mechanical engineering.
• Nova feature on Artificial Life
• Dynamic Programming
• Richard Bellman Biography
• Tutorial
• Course Xserve G5 cluster
• Xserve G5 cluster
• Bioinformatics Cluster
• Xgrid
• Xgrid job submission instructions
• Analysis tools