1 / 11

Bioinformatics Chem 434

Bioinformatics Chem 434. Dr. Nancy Warter-Perez Computer Engineering Dr. Jamil Momand Chemistry & Biochemistry. What is Bioinformatics?. Fredj Tekaia at the Institut Pasteur offers this definition of bioinformatics:

foster
Download Presentation

Bioinformatics Chem 434

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. BioinformaticsChem 434 Dr. Nancy Warter-Perez Computer Engineering Dr. Jamil Momand Chemistry & Biochemistry

  2. What is Bioinformatics? • Fredj Tekaia at the Institut Pasteur offers this definition of bioinformatics: "The mathematical, statistical and computing methods that aim to solve biological problems using DNA and amino acid sequences and related information."

  3. Classical Bioinformatics • According to Damian Counsell from bioinformatics.org “use computers to store, retrieve, analyze or predict the composition or the structure of biomolecules. As computers become more powerful you could probably add simulate to this list of bioinformatics verbs. "Biomolecules" include your genetic material---nucleic acids---and the products of your genes: proteins. These are the concerns of "classical" bioinformatics, dealing primarily with sequence analysis.”

  4. “New” Bioinformatics • comparative genomics - look for differences and similarities between all the genes of multiple species • functional genomics - identifying gene functions and associations • proteomics - catalogue the activities and characterize interactions between all gene products (in humans) • structural genomics - crystallize and or predict the structures of all proteins (in humans)

  5. Chem 434 Objectives Chemist/Biologist Perspective • Understand how to use existing bioinformatics software to • Retrieve gene sequence information from Genbank • Conduct similarity searches using BLAST • Align multiple sequences with Clustal W • Predict protein functional motifs with BLOCKS and ProDom • Display and compare 3-D protein structures

  6. Chem 434 Objectives Computer Scientist/Mathematician Perspective • Develop algorithms for sequence analysis • Write programs using Python scripting language • Understand statistics used to align sequences

  7. What is Python? • A portable, interpretive, object-oriented programming language • Elegant syntax • Powerful high-level built-in data types • Numbers, strings, lists, dictionaries • Full set of string operations

  8. Why Python? • Previously used C++ • Scripting languages useful for bioinformatics • Perl is “bioinformatics standard” • Python is more “robust” for larger software projects

  9. Useful Tutorials • DNA from the Beginning • http://www.dnaftb.org/dnaftb/ • Python Tutorial • http://www.python.org/doc/current/tut/tut.html

  10. Python Development Open-Source Software • Python interpreter - will run on windows, you need to download it in two parts: 1. the actual interpreter and core of python http://www.python.org/2.3.3/ (get the Python-2.3.3.exe file) 2. a (very nice!) integrated development environment for python called pythonwin, by Mark Hammond http://starship.python.net/crew/mhammond/win32/Downloads.html

More Related