Stothard Research Group


We have completed sequencing of more than 400 cattle genomes!


AN SC 484 - Animal Molecular Biology. This course should enable the student to gain a solid understanding of the major approaches and methodologies of applied molecular biotechnology in animal science. The student should become familiar with the terminology associated with this research area that will allow them to understand and critically evaluate the current literature. Specifically, the selected research papers that are presented and discussed in class and the major term paper are intended to develop in the student the ability to concisely summarize and critically evaluate scientific publications.

AFNS 460 - Applied Bioinformatics. Introduction to databases, software tools, and analysis methods used to characterize DNA and protein sequences. Topics include information retrieval from sequence databases, protein function prediction, assessing sequence similarity, biological pathway analysis, measuring gene expression, proteomics, and protein identification.

AN SC 479/AN SC 499 - Integrative Problem Solving Project in Animal Science and Animal Health. Students complete an applied research project that involves writing a proposal, conducting research, performing statistical analyses, preparing a scientific manuscript, and presenting the results in a public forum.

BIOIN 301/BIOL 501 - Bioinformatics I. Introduction to computational tools and databases used in the collection and analysis of sequence data and other analytical data from high-throughput molecular biology studies. Students will use existing tools, learn the underlying algorithms and their limitations, and will write programs to perform bioinformatic analysis.

GENET 510 - Advanced Topics in Gene Regulation, Development and Medical Genetics. Directed study of literature on regulation of the phenotypic expression of genes and the manner in which genes direct the process of development.


Linux for bioinformatics - an introduction to the use of Linux for bioinformatics. This guide describes how to access a Linux user account, basic shell commands, permissions, redirecting output, piping output, working with tar and zip files, copying files to a Linux account, the Linux file system, EMBOSS, clustalw, remote_blast_client.pl, the .bashrc file, vi, and shell scripts.
Written by: Paul Stothard.
Download: linux_for_bioinformatics.pdf.

Programming in Perl - these collections of simple programs are intended to introduce the Perl programming language to students with little or no programming experience. Detailed comments inside the programs describe what each line of code does when executed. Students are encouraged to type (without the comments), edit, and run these programs. By doing so they will become familiar with the notations used by Perl, and the error messages that arise from common typos. Note that these programs are not meant to illustrate the best way to complete a particular task. Several features of Perl have been omitted for the sake of simplicity. Students may wish to write faster or more compact versions of these programs using subroutines, objects, or more complex regular expressions.
Written by: Paul Stothard.
Download: learning_perl_tutorial_part_I.zip, learning_perl_tutorial_part_II.zip, learning_perl_tutorial_part_III.zip.