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(The University of Akron)

The University of Akron is a coeducational public research university located in Akron, Ohio, part of the University System of Ohio. It was founded in 1870 as a small college affiliated with the Universalist Church. In 1913 ownership was transferred to the City of Akron. In 1967 the university became a state institution. The University of Akron is regarded as a world leader in polymer research. As a STEM-focused institution, it focuses on industries such as polymers, advanced materials, and engineering. In the last decade it has sought to increase its research portfolio and gain recognition for its productivity in technology transfer and commercialization.

More information: http://en.wikipedia.org/wiki/University_of_Akron

Deer-Vehicle Crashes Hui Anne Ben

Deer-Vehicle Crashes Hui Anne Ben
The Highs and Lows of PITCH Presented By Chris McVay Grade 3-General Music

The Highs and Lows of PITCH Presented By Chris McVay Grade 3-General Music
Holt H.S. General Music Section A. Intro to Opera Chapter 14 from Opera for Dummies

Holt H.S. General Music Section A. Intro to Opera Chapter 14 from Opera for Dummies

The Ten Most Common Misconceptions about Opera Day One With Mr. Lange
Scales & Intervals Theory I 9th grade Ms. Wasko

Scales & Intervals Theory I 9th grade Ms. Wasko
PRESENTATION METHODS 6800:680

PRESENTATION METHODS 6800:680
Programming and Perl for Bioinformatics Part I

Programming and Perl for Bioinformatics Part I
Microarray Data Analysis

Microarray Data Analysis

Data preprocessing and visualization Supervised learning Machine learning approaches Unsupervised learning Clustering and pattern detection Gene regulatory regions predictions based co-regulated genes Linkage between gene expression data and gene sequence/function databases …

Developed by Nick Ciulli Andrea Cassidy Cathie Petrus Linda Imhoff Species of plants and animals are disappearing from the earth at an alarming rate. In the United States alone, there are 568 threatened or endangered animal and 746 plant species. (http://ecos.fws.gov/tess_public/SummaryStatistics.do) In Ohio, 24 plants and animals are threatened or endangered Organizations are trying to stop the destruction of rainforests, wetlands, and other native habitats where endangered animals live. Other organizations are trying to protect species from overexploitation and repopulate areas the animals were originally from. http://www.iucnredlist.org/info/gallery2006
Definitions

Definitions

Optimal alignment - one that exhibits the most correspondences. It is the alignment with the highest score. May or may not be biologically meaningful. Global alignment - Needleman-Wunsch (1970) maximizes the number of matches between the sequences along the entire length of the sequences. Local alignment - Smith-Waterman (1981) gives the highest scoring local match between two sequences.
Roadmap

Roadmap

The topics: basic concepts of molecular biology more on Perl overview of the field biological databases and database searching sequence alignments phylogenetics structure prediction microarray data analysis
DNA microarray and array data analysis

DNA microarray and array data analysis

Some of the slides are adapted from the lecture notes of Dr. Patrick Leahy of the Gene Expression Array Core Facility at CWRU
Protein Structure Databases

Protein Structure Databases

Databases of three dimensional structures of proteins, where structure has been solved using X-ray crystallography or nuclear magnetic resonance (NMR) techniques Protein Databases: PDB (protein data bank) Swiss-Prot PIR (Protein Information Resource) SCOP (Structural Classification of Proteins)
Microarray Data Analysis

Microarray Data Analysis

Data preprocessing and visualization Supervised learning Machine learning approaches Unsupervised learning Clustering and pattern detection Gene regulatory regions predictions based co-regulated genes Linkage between gene expression data and gene sequence/function databases …
Where to get Perl ?

Where to get Perl ?

Visit the class web site for the links! www.perl.com / www.perl.org Unix/Linux/Solaris Interpreter (called “perl”) comes pre-installed usually Get source from www.perl.com Win32 Get source distribution from www.perl.com Have to compile Get binary from www.activestate.com No need to compile, runs pretty well Macintosh www.macperl.com Perl IDE (integrated development environment) Open Perl IDE (Jurgen Guntherodt) It’s mainly an editor. ActiveState Komodo 3.0 (IDE for Perl, Python, Tcl, …) $29.95 for a student license
DNA microarray and array data analysis

DNA microarray and array data analysis

Some of the slides are adapted from Dr. Patrick Leahy of the Gene Expression Array Core Facility at CWRU
Topics

Topics

The topics: basic concepts of molecular biology more on Perl overview of the field biological databases and database searching sequence alignments phylogenetic trees protein structure prediction microarray data analysis
Flow chart of Affymetrix from sample to information

Flow chart of Affymetrix from sample to information

Generate Affy.dat file Hyb. cRNA Hybridize to Affy arrays Output as Affy.chp file Text Self Organized Maps (SOMs) Functional annotation Pathway assignment Co-ordinate regulation Promoter motif commonalities Tissue
Roadmap

Roadmap

The topics: basic concepts of molecular biology more on Perl overview of the field biological databases and database searching sequence alignments phylogenetics structure prediction microarray data analysis
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