STORI: selectable taxon ortholog retrieval iteratively

Stern, Joshua Gallant

Title:

STORI: selectable taxon ortholog retrieval iteratively

dc.contributor.advisor	Gaucher, Eric A.
dc.contributor.author	Stern, Joshua Gallant
dc.contributor.committeeMember	Hammer, Brian K.
dc.contributor.committeeMember	Dunham, Christine M.
dc.contributor.committeeMember	Jordan, Irving K.
dc.contributor.committeeMember	Snell, Terry W.
dc.contributor.department	Biology
dc.date.accessioned	2015-06-08T17:51:00Z
dc.date.available	2015-06-08T17:51:00Z
dc.date.created	2013-12
dc.date.issued	2013-08-07
dc.date.submitted	December 2013
dc.date.updated	2015-06-08T17:51:00Z
dc.description.abstract	Speciation and gene duplication are fundamental evolutionary processes that enable biological innovation. For over a decade, biologists have endeavored to distinguish orthology (homology caused by speciation) from paralogy (homology caused by duplication). Disentangling orthology and paralogy is useful to diverse fields such as phylogenetics, protein engineering, and genome content comparison. A common step in ortholog detection is the computation of Bidirectional Best Hits (BBH). However, we found this computation impractical for more than 24 Eukaryotic proteomes. Attempting to retrieve orthologs in less time than previous methods require, we developed a novel algorithm and implemented it as a suite of Perl scripts. This software, Selectable Taxon Ortholog Retrieval Iteratively (STORI), retrieves orthologous protein sequences for a set of user-defined proteomes and query sequences. While the time complexity of the BBH method is O(#taxa^2), we found that the average CPU time used by STORI may increase linearly with the number of taxa. To demonstrate one aspect of STORI’s usefulness, we used this software to infer the orthologous sequences of 26 ribosomal proteins (rProteins) from the large ribosomal subunit (LSU), for a set of 115 Bacterial and 94 Archaeal proteomes. Next, we used established tree-search methods to seek the most probable evolutionary explanation of these data. The current implementation of STORI runs on Red Hat Enterprise Linux 6.0 with installations of Moab 5.3.7, Perl 5 and several Perl modules. STORI is available at: <http://github.com/jgstern/STORI>.
dc.description.degree	M.S.
dc.format.mimetype	application/pdf
dc.identifier.uri	http://hdl.handle.net/1853/53377
dc.language.iso	en_US
dc.publisher	Georgia Institute of Technology
dc.subject	Ortholog prediction
dc.subject	Protein sequence retrieval
dc.subject	Modeling bacterial evolution
dc.subject	Fusobacteria
dc.subject	Molecular sequence data management
dc.subject	Bayesian inference phylogenomics
dc.title	STORI: selectable taxon ortholog retrieval iteratively
dc.type	Text
dc.type.genre	Thesis
dc.type.genre	Thesis
dspace.entity.type	Publication
local.contributor.corporatename	College of Sciences
local.contributor.corporatename	School of Biological Sciences
relation.isOrgUnitOfPublication	85042be6-2d68-4e07-b384-e1f908fae48a
relation.isOrgUnitOfPublication	c8b3bd08-9989-40d3-afe3-e0ad8d5c72b5
thesis.degree.level	Masters