BIOINFORMATICS PROGRAM

St. Edward’s University• Genomics Education Partnership (GEP)• Genomics Consortium for Active Teaching (GCAT)

Curriculum Genomics Track (11-12hrs):EvolutionBiochemistry I, IICell, Micro, Neuro

Bio-Math Track Track (11-12hrs):Linear AlgebraDifferential EquationProb/Theory Stats.Cell, Micro, Neuro

Cells/Org. Sys.

Organisms/Pop

Gen. Chem

Analytic Chem

Calculus I

Calculus II

Intro BINF

Y1

Molecular

Organic I

Java I

Calculus III

Discrete

Java II

Genomics

Perl, Python, R

Y2

Applied Stats

Alg. & Data Struct.

Senior Seminar

Res

earc

h (3

x)

BioinformaticsY3,4

Biological Programming

Data structures: scalars, arrays, hashesControl StructuresBlast: principles, parsing (BioPerl)Distance matrices: dissimilarity (Jaccard)Phylogenetic Profiles• Protein conservation/annotation

Phylogenetic Profiles

Bioinformatics

Construct simple hidden Markov model

Membrane Proteins:LILWLVIAVVLMSVFQSFGPPSLLASIFISWFPMLLLIGVWIFFMYFVIQTYLPCIMTVILSQVSFW

Soluble Proteins:MAKNRQMQGGGGKGAMSFGKSKARMLTEDQIKTTFADVAGCDEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEAKVPF

State Sequences:>FTSH_ECOLIiiiiMMMMMMMMMMMMMMMMMMMMooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooMMMMMMMMMMMMMMMMMMMMMIiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii

Other Projects:• Smith-Waterman• Multivariate Analysis (PCoA)• RNASeq Analysis (Tophat/Bowtie)

Senior Research Projects

No Burn

Light Burn

High Burn

Unweighted (rare species)

Isolate DNA PCR 454 SequencingPrimer Sets

Soil samples

QIIME Sequence Filtering • depleted of barcodes/ primers• < 200 removed• Ave. quality score <25• Ambiguous base calls• Homopolymer runs (>6x)• Chimeras

OTU Identification Clustering at 3% divergence (97% similarity)

OTU Classification Sequences were aligned to the Silva database using the PyNAST algorithm (minimum percent identity was set at 80%)