This Is AuburnElectronic Theses and Dissertations

Elucidating Biological Questions with Bioinformatics Tools, with a Case Study of Tube Worm Hemoglobin




Waits, Damien

Type of Degree

Master's Thesis


Biological Sciences


The goal of my Master’s Thesis research was to utilize sequenced data in conjunction with new data to investigate the sulfur binding hemoglobin of the annelid family Siboglinidae. To accomplish this, multiple bioinformatic scripts were developed to help streamline the process of isolating and analyzing hemoglobin sequence data. Given the large amount of sequence data, bioinformatics pipelines are necessary to efficiently clean, sort, and analyze the information. Siboglinidae is a group of annelids living in chemosynthetic environments that has been studied extensively. Their unique symbiosis facilitated by sulfur-binding hemoglobin is shared by all members except the genus Osedax. Using the available and newly generated sequence data, we sought to determine if Osedax possessed the genetic machinery capable of producing sulfur- binding hemoglobin using a bioinformatics approach. During this study, multiple scripts were written to efficiently analyze the data. Some of these larger programs that have since been included in pipelines used to explore animal phylogeny. Herein, I describe my research on the hemoglobin of the siboglinids and the bioinformatics tools that have resulted. Chapter 1 describes my research on siboglinid hemoglobin and corresponds to a manuscript submitted to the Journal of Molecular Evolution. Chapter 2 reports on two bioinformatic programs that were used in a phylogenomic pipeline implemented by members of our research group.