1. Doug Raiford Lesson 3

2.  More and more sequence data is being generated every day  Useless if not made available to other researchers

3.  Not just sequence data  Many other biological experiments  Expression  NMR  Mass Spec  Protein X-ray crystallography

4.  With the data comes scientific journal articles

5.  Search tools  Find similar genes in other organism  Find articles  Find  Implemented algorithms  Alignment  Sequence assembly  Protein structure prediction

6.  National Center for Biotechnology Information (NCBI) National Center for Biotechnology Information (NCBI)  GenBank (accessed through NCBI) ▪ Sponsored by National Institute of Health (NIH)  RefSeq ▪ Derived from GenBank, curated, non-redundant

7.  European Molecular Biology Laboratory (EMBL)  DNA Data Bank of Japan (DDBJ)

8.  Protein Data Bank (PDB)  PDB files: standardized format for viewers  Protein Information Resource (PIR)

9.  Will revisit later  Can actually perform scientific analysis  Color by charge  Hydrophobicity  Render surface

10.  Entrez  Global Query Cross-Database Search System  Single source for searching publications, sequences, proteins, diseases, etc.  Whole Genome DB  Genomic Expression Omnibux (GEO)  Online Mendelian Inheritance in Man (OMIM)  PubMed  Map of site

11.  Practical Extraction and Report Language  Expansion came later  Really good at string manipulation  DNA and proteins represented as strings  Scripting language  Almost all Unix and Linux systems come with it installed  Free download and install for windows

12.  Make a computer do what we want it to do  Program in a language  Machine language ▪ Low level—1’s and 0’s  High level programming language ▪ C/C++ ▪ Java ▪ Compiled into machine language  Very high level languages ▪ Scripting ▪ Interpreted Perl lives here

13.  Display something to the screen  Syntax and punctuation  Store something in a variable  Commenting the code  Some easy string manipulation print “Hello World\n”;