Doug RaifordLesson 3

More and more sequence data is being generated every day

Useless if not made available to other researchers

Not just sequence dataMany other biological

experiments Expression NMR Mass Spec Protein X-ray crystallography

With the data comes scientific journal articles

Search tools Find similar genes in other

organism Find articles Find

Implemented algorithms Alignment Sequence assembly Protein structure prediction

National Center for Biotechnology Information (NCBI) GenBank

(accessed through NCBI)▪ Sponsored by

National Institute of Health (NIH)

RefSeq▪ Derived from

GenBank, curated, non-redundant

European Molecular Biology Laboratory (EMBL)

DNA Data Bank of Japan (DDBJ)

Protein Data Bank (PDB) PDB files: standardized format for

viewersProtein Information Resource (PIR)

Will revisit laterCan actually perform scientific

analysis Color by charge Hydrophobicity Render surface

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

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

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 herePerl lives here

Display something to the screenSyntax and punctuationStore something in a variableCommenting the codeSome easy string manipulation

print “Hello World\n”;