Doug Raiford Lesson 3

mewstennisSoftware and s/w Development

Nov 4, 2013 (3 years and 9 months ago)

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Doug Raiford

Lesson 3


More and more
sequence data is
being generated
every day


Useless if not made
available to other
researchers


Not just sequence data


Many 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 viewers


Protein Information Resource (PIR)


Will revisit later


Can 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 here


Display something to the screen


Syntax and punctuation


Store something in a variable


Commenting the code


Some easy string manipulation

print “Hello World
\
n”;