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2 Οκτ 2013 (πριν από 3 χρόνια και 10 μήνες)

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A Bridge to Bioinformatics Tools

Introducing Programming in Genetics Classes

Ogun

Adebali
, Ed
Himelblau
,
Ioannis

Tsiligaridis

A Bridge to Bioinformatics Tools

Goals:

-
Reinforce material learned in the genetics
c
ourse

-
Introduce
a
lgorithm thinking

-
Introduce computation for biological problems

-
Bridge genetics to bioinformatics tools

A Bridge to Bioinformatics Tools

Philosophy:

It is important for students to make connections
between classical and molecular genetics.


Exposure to programing using the genetic code will
introduce students to bioinformatics concepts
central to modern biology.


Low barrier to implementation…it should fit easily
into a genetics course and take little time

(1 lecture + 1 homework).

(but can be expanded to more complex questions…)


A Bridge to Bioinformatics Tools

Resources:

-
Instructor Guide

-
PERL code for aligning sequences

-
FASTA files

Round/Winkled Peas

(
SBE1

WT and mutant alleles)

Sickle Cell Anemia

(
HBB

WT and mutant alleles)

*

*

* Common examples in genetics courses

A Bridge to Bioinformatics Tools

Description:

Pea shape and sickle cell anemia are both cases in
which
wildtype

and mutant alleles have unique
phenotypes.


Students study the inheritance of these alleles.


Students will write a program to compare
wildtype

and mutant sequence to discover the DNA changes
that underlie the phenotypes.


A Bridge to Bioinformatics Tools

Programming is useful:

An introduction to algorithmic thinking in general is offered for
student preparation in programming.


The problem of two
-
sequence alignment (global/local) will be
examined and a solution in PERL will be given (With/without gaps).


Early exposure of biologists to these ideas could influence attitudes
toward using programming in future plans.



We prefer to work with PERL because of the relatively easy syntax
and steps of programming.


Profile/consensus will be examined

depending on time.