A Bridge to Bioinformatics ToolsIntroducing Programming in Genetics Classes

Ogun Adebali, Ed Himelblau, Ioannis Tsiligaridis

A Bridge to Bioinformatics Tools

Goals:

-Reinforce material learned in the genetics course

-Introduce algorithm 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)

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* 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 examineddepending on time.