Transcript Biology and computers

Course Summary
November 29, 2012
 Course
summary
 Instructor evaluations
 Programming Workshop
Course Summary
Course Learning Objectives (from course syllabus):
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Retrieve gene sequence information from GenBank.
Understand the theory that led to the development of scoring
methods commonly used to measure sequence similarities.
Use BLAST to conduct gene similarity searches.
Align multiple sequences with Clustal W software.
Predict secondary structures with PSIPRED.
Display and compare protein structures.
Write software programs that queries a database with a
protein sequence.
List of software programs you
should be familiar with
Dotter
Global sequence
alignment
Smith-Waterman local
sequence alignment
BLAST
PSI-BLAST
CLUSTAL W
Kyte-Doolittle
(hydrophobicity)
PSIPRED
List of databases that we studied
Online Mendelian
Inheritance of Man
GenBank
Protein Data Bank
(PDB)
PubMed
Concepts in bioinformatics
Scoring alignments
Modular nature of proteins
Sliding window
Alignment methods (Local vs. Global)
Dynamic programming
Statistics (E-value)
Concepts in bioinformatics II
Primary and secondary databases
Similar and identical amino acids
Substitution matrices (PAM, BLOSUM,
PSSM)
Neural networks
Protein structure prediction
Create a software program that aligns
sequences based on substitution matrices
Future of bioinformatics
Traditionally divided into
two camps-users and
developers
CSULA students should
have an advantage over
applicants to graduate
schools and over
applicants to job openings
in the bioinformatics
sector
Extra Questions for Instructor
Evaluation
Please answer the following in your comments:
1) This course will help you further your career.
2) The programming component increased your understanding of
the field of bioinformatics.
3) The course workload, compared to other 4 unit science classes,
was (a) too heavy, (b) too light, (c) just right.
4) What prerequisite courses would help you increase your
performance in this course?
5) What components of the bioinformatics field would you like to
see expanded into a second, more advanced, course?
6) The book helped your understanding of the material.