Genetics and Genomics Commons^™

Cell-Free Circulating Mirna Biomarkers In Cancer., Meng-Hsuan Mo, Liang Chen, Yebo Fu, Wendy Wang, Sidney W. Fu

Microbiology, Immunology, and Tropical Medicine Faculty Publications

Considerable attention and an enormous amount of resources have been dedicated to cancer biomarker discovery and validation. However, there are still a limited number of useful biomarkers available for clinical use. An ideal biomarker should be easily assayed with minimally invasive medical procedures but possess high sensitivity and specificity. Commonly used circulating biomarkers are proteins in serum, most of which require labor-intensive analysis hindered by low sensitivity in early tumor detection. Since the deregulation of microRNA (miRNA) is associated with cancer development and progression, profiling of circulating miRNAs has been used in a number of studies to identify novel minimally …

Phylogenetic Search Through Partial Tree Mixing., Kenneth Sundberg, Mark Clement, Quinn Snell, Dan Ventura, Michael Whiting, Keith Crandall

Computational Biology Institute

BACKGROUND: Recent advances in sequencing technology have created large data sets upon which phylogenetic inference can be performed. Current research is limited by the prohibitive time necessary to perform tree search on a reasonable number of individuals. This research develops new phylogenetic algorithms that can operate on tens of thousands of species in a reasonable amount of time through several innovative search techniques.

RESULTS: When compared to popular phylogenetic search algorithms, better trees are found much more quickly for large data sets. These algorithms are incorporated in the PSODA application available at http://dna.cs.byu.edu/psoda

CONCLUSIONS: The use of Partial Tree Mixing …

Pomc Is Expressed In Pancreatic Alpha Cells, Samia M.M Farrara

Electronic Theses and Dissertations

Pancreatic alpha cells secrete glucagon to increase blood glucose during hypoglycemia. Currently, the mechanisms that initiate glucagon secretion are not well understood. This study investigates the expression of pro-opiomelanocortin (POMC), a potent regulator of glucagon secretion, in alpha cells.

Insulin tolerance tests in mice lacking the POMC gene showed a correlation between alpha MSH, and glucagon secretion from alpha cells (Hochgeschwender et al. 2003). Results from a previous study showed that the POMC product, melanocortin á-MSH, acts through a melanocortin receptor 4 (MC4R) at the surface of the alpha cells to trigger the release of glucagon [Angleson, unpublished data, Lumsden …

Novel Report Of Expression And Function Of Cd97 In Malignant Gliomas: Correlation With Wilms Tumor 1 Expression And Glioma Cell Invasiveness Laboratory Investigation, Archana Chidambaram, Helen L. Fillmore, Timothy E. Van Meter, Catherine I. Dumur, William C. Broaddus

Division of Research and Economic Development Faculty & Staff Publications

Object. The Wilms tumor 1 (WT1) protein—a developmentally regulated transcription factor—is aberrantly expressed in gliomas and promotes their malignant phenotype. However, little is known about the molecular allies that help it mediate its oncogenic functions in glioma cells.

Methods. The authors used short interfering RNA (siRNA) to suppress WT1 expression in glioblastoma (GBM) cells and evaluated the effect of this on GBM cell invasiveness. Gene expression analysis was then used to identify the candidate genes that were altered as a result of WT1 silencing. One candidate target, CD97, was then selected for further investigation into its role by suppressing …

Inheritance Of Humeral Spotting In The Croaking Gourami (Osphronemidae: Trichopsis Vittatus), Jack Frankel, Lisa Alder-Golden, Andre Porter

Department of Biology Faculty Publications

The croaking gourami (Trichopsis vittatus) exhibits two phenotypes associated with humeral spotting. Fish possess a prominent, dark humeral patch or spot located behind the operculum or lack this spotting pattern. Segregation patterns observed from the progenies of eleven different crosses support the hypothesis that the inheritance of humeral spotting in T. vittatus is controlled by the action of a single autosomal locus, with complete dominance of the allele controlling the spotted phenotype.

Effects Of Feeding Field Peas In Combination With Distillers Grains Plus Solubles In Finishing And Growing Diets On Cattle Performance And Carcass Characteristics, A. C. Pesta, A. H. Titlow, J. A. Hansen, A. L. Berger, S. A. Furman, Matt K. Luebbe, G. E. Erickson, K. H. Jenkins

Department of Animal Science: Faculty Publications

Two studies were conducted to evaluate field peas and wet or dry corn distillers grains with solubles (WDGS and DDGS, respectively) in finishing and growing diets. In Exp. 1, British crossbred steers (n = 352, initial BW 356 ± 27 kg) were used in a randomized block design with factors being 0 or 20% field peas and 0 or 30% WDGS in dry-rolled corn (DRC) based finishing diets (DM basis). There was an interaction (P < 0.01) for DMI and G:F. Feeding WDGS increased ADG (P < 0.01), whereas peas had no effect on ADG (P = 0.33). Including WDGS increased G:F in diets without peas (P < 0.01), but had no impact (P = 0.12) in diets containing peas. Peas increased G:F (P = 0.04) in diets without WDGS, but decreased G:F (P = 0.03) with WDGS. Feeding WDGS increased HCW (P < 0.01). In Exp. 2, Continental crossbred heifers (yr. 1; n = 108, initial BW 338 ± 14 kg) and British crossbred steers (yr. 2; n = 90, initial BW 321 ± 10 kg) were assigned randomly to 1 of 9 pastures. Treatments were supplementation with loose DDGS meal on the ground (GROUND), in a bunk (BUNK) or a 25% field peas, 75% DDGS cube on the ground (CUBE) at equal CP. Final BW and ADG were less (P < 0.01) for GROUND than for CUBE and BUNK, which were similar. These data indicate up to 50% DRC could be replaced by peas and WDGS, and peas are an acceptable binder for DDGS range cubes.

A Systematic Genetic Screen To Dissect The Microrna Pathway In Drosophila, Sigal Pressman, Catherine A. Reinke, Xiaohong Wang, Richard W. Carthew

Faculty Publications

A central goal of microRNA biology is to elucidate the genetic program of miRNA function and regulation. However, relatively few of the effectors that execute miRNA repression have been identified. Because such genes may function in many developmental processes, mutations in them are expected to be pleiotropic and thus are discarded in most standard genetic screens. Here, we describe a systematic screen designed to identify all Drosophila genes in ~40% of the genome that function in the miRNA pathway. To identify potentially pleiotropic genes, the screen analyzed clones of homozygous mutant cells in heterozygous animals. We identified 45 mutations representing …

Testing Phylogenetic Hypotheses Of The Subgenera Of The Freshwater Crayfish Genus Cambarus (Decapoda: Cambaridae)., Jesse W Breinholt, Megan L Porter, Keith A Crandall

Computational Biology Institute

BACKGROUND: The genus Cambarus is one of three most species rich crayfish genera in the Northern Hemisphere. The genus has its center of diversity in the Southern Appalachians of the United States and has been divided into 12 subgenera. Using Cambarus we test the correspondence of subgeneric designations based on morphology used in traditional crayfish taxonomy to the underlying evolutionary history for these crayfish. We further test for significant correlation and explanatory power of geographic distance, taxonomic model, and a habitat model to estimated phylogenetic distance with multiple variable regression.

METHODOLOGY/PRINCIPAL FINDINGS: We use three mitochondrial and one nuclear gene …

A Genomic Island In Salmonella Enterica Ssp. Salamae Provides New Insights On The Genealogy Of The Locus Of Enterocyte Effacement., P Scott Chandry, Simon Gladman, Sean C Moore, Torsten Seemann, Keith A Crandall, Narelle Fegan

Computational Biology Institute

The genomic island encoding the locus of enterocyte effacement (LEE) is an important virulence factor of the human pathogenic Escherichia coli. LEE typically encodes a type III secretion system (T3SS) and secreted effectors capable of forming attaching and effacing lesions. Although prominent in the pathogenic E. coli such as serotype O157:H7, LEE has also been detected in Citrobacter rodentium, E. albertii, and although not confirmed, it is likely to also be in Shigella boydii. Previous phylogenetic analysis of LEE indicated the genomic island was evolving through stepwise acquisition of various components. This study describes a new LEE region from two …

A High Density Snp Array For The Domestic Horse And Extant Perissodactyla: Utility For Association Mapping, Genetic Diversity, And Phylogeny Studies, Molly E. Mccue, Danika L. Bannasch, Jessica Lynn Petersen, Jessica Gurr, Ernie Bailey, Matthew M. Binns, Ottmar Distl, Gérard Guérin, Telhisa Hasegawa, Emmeline W. Hill, Tosso Leeb, Gabriella Lindgren, M. Cecilia T. Penedo, Knut H. Røed, Oliver A. Ryder, June E. Swinburne, Teruaki Tozaki, Stephanie J. Valberg, Mark Vaudin, Kerstin Lindblad-Toh, Claire M. Wade, James R. Mickelson

Department of Animal Science: Faculty Publications

An equine SNP genotyping array was developed and evaluated on a panel of samples representing 14 domestic horse breeds and 18 evolutionarily related species. More than 54,000 polymorphic SNPs provided an average inter-SNP spacing of ~43 kb. The mean minor allele frequency across domestic horse breeds was 0.23, and the number of polymorphic SNPs within breeds ranged from 43,287 to 52,085. Genome-wide linkage disequilibrium (LD) in most breeds declined rapidly over the first 50–100 kb and reached background levels within 1–2 Mb. The extent of LD and the level of inbreeding were highest in the Thoroughbred and lowest in the …

Index Selection In Terminal Sires Improves Early Lamb Growth, G. C. Márquez, W. Haresign, M. H. Davies, G. C. Emmans, Rainer Roehe, L Bünger, G. Simm, Ronald M. Lewis

Department of Animal Science: Faculty Publications

The use of terminal sires (TS) for crossbreeding is integral to the UK sheep industry where approximately 71% of market lambs are sired by TS rams. Early growth of these crossbred lambs affects profitability. The objectives of this study were i) to evaluate the effectiveness of index selection among TS on BW and ADG of their crossbred offspring; and ii) to compare the efficacy of that selection within TS breeds. The most widely used TS breeds in the United Kingdom are Charollais, Suffolk, and Texel. These participated in sire referencing schemes in which they were evaluated on a lean growth …

Dried Distillers Grains As A Substitute For Grazed Forage, L. A. Stalker, T. J. Klopfenstein, Walter H. Schacht, J. D. Volesky

Department of Animal Science: Faculty Publications

A 2-yr study evaluated effects of feeding dried distillers grains (DDG) to yearlings grazing native range at greaterthan- recommended stocking rates on BW gain, grazed forage quality, and forage disappearance. Thirty-six paddocks were assigned randomly to 1 of 3 treatments: 1) control, stocked at a moderate stocking rate (1.48 animal unit months/ha in yr 1, 1.06 animal unit months/ha in yr 2) with no DDG; 2) double stocked, in which stocking rate was exactly twice the control with no DDG; and 3) double stocked with 2.27 kg/d (DM) of DDG per animal. Six paddocks per treatment replication were grazed in …

Genetic Parameter Estimates For Calving Difficulty And Birth Weight In A Multi-Breed Population, C. M. Ahlberg, L. A. Kuehn, R. M. Thallman, Stephen D. Kachman, M. L. Spangler

Department of Animal Science: Faculty Publications

Birth weight (BWT) and calving difficulty (CD) were recorded on 4,580 first parity females from the Germplasm Evaluation (GPE) program at the U.S. Meat Animal Research Center. Both traits were analyzed using a bivariate animal model with direct and maternal effects. Genetic groups for breed of AI sire were fitted to estimate breed differences. Bos Indicus influenced breeds tended to have the largest BWT. Heritability estimates for BWT direct, CD direct, BWT maternal and CD maternal were 0.45 (0.09), 0.40 (0.09), 0.18 (0.08), and 0.18 (0.08), respectively. Genetic correlation estimates were positive between direct BWT and CD direct at 0.82 …

Murine Gut Microbiota Is Defined By Host Genetics And Modulates Variation Of Metabolic Traits, Autumn M. Mcknite, Maria Elisa Perez-Munoz, Lu Lu, Evan G. Williams, Simon Brewer, Penelope A. Andreux, John W. M. Bastiaansen, Xusheng Wang, Stephen D. Kachman, Johan Auwerx, Robert W. Williams, Andrew K. Benson, Daniel A. Peterson, Daniel C. Ciobanu

Department of Animal Science: Faculty Publications

The gastrointestinal tract harbors a complex and diverse microbiota that has an important role in host metabolism. Microbial diversity is influenced by a combination of environmental and host genetic factors and is associated with several polygenic diseases. In this study we combined next-generation sequencing, genetic mapping, and a set of physiological traits of the BXD mouse population to explore genetic factors that explain differences in gut microbiota and its impact on metabolic traits. Molecular profiling of the gut microbiota revealed important quantitative differences in microbial composition among BXD strains. These differences in gut microbial composition are influenced by host-genetics, which …

Congenic Strain Analysis Reveals Genes That Are Rapidly Evolving Components Of A Prezygotic Isolation Mechanism Mediating Incipient Reinforcement, Christina M. Laukaitis, Corina Mauss, Robert C. Karn

Scholarship and Professional Work - LAS

Two decades ago, we developed a congenic strain of Mus musculus, called b-congenic, by replacing the androgen-binding protein Abpa27^a allele in the C3H/HeJ genome with the Abpa27^b allele from DBA/2J. We and other researchers used this b-congenic strain and its C3H counterpart, the a-congenic strain, to test the hypothesis that, given the choice between signals from two strains with different a27 alleles on the same genetic background, test subjects would prefer the homosubspecific one. It was our purpose in undertaking this study to characterize the segment transferred from DBA to the C3H background in producing the b-congenic …

The Roles Of Gene Duplication, Gene Conversion And Positive Selection In Rodent Esp And Mup Pheromone Gene Families With Comparison To The Abp Family, Robert C. Karn, Christina M. Laukaitis

Scholarship and Professional Work - LAS

Three proteinaceous pheromone families, the androgen-binding proteins (ABPs), the exocrine-gland secreting peptides (ESPs) and the major urinary proteins (MUPs) are encoded by large gene families in the genomes of Mus musculus and Rattus norvegicus. We studied the evolutionary histories of the Mup and Esp genes and compared them with what is known about the Abp genes. Apparently gene conversion has played little if any role in the expansion of the mouse Class A and Class B Mup genes and pseudogenes, and the rat Mups. By contrast, we found evidence of extensive gene conversion in many Esp genes although …

The Role Of Epigenetics In Evolution: The Extended Synthesis, Aaron W. Schrey, Christina L. Richards, Victoria Meller, Vincent Sollars, Douglas M. Ruden

Integrative Biology Faculty and Staff Publications

No abstract provided.

Epigenetic Variation May Compensate For Decreased Genetic Variation With Introductions: A Case Study Using House Sparrows (Passer Domesticus) On Two Continents, Aaron W. Schrey, Courtney A. C. Coon, Michael T. Grispo, Mohammed Awad, Titus Imboma, Earl D. Mccoy, Henry R. Mushinsky, Christina L. Richards, Lynn B. Martin

Integrative Biology Faculty and Staff Publications

Epigenetic mechanisms impact several phenotypic traits and may be important for ecology and evolution. The introduced house sparrow (Passer domesticus) exhibits extensive phenotypic variation among and within populations. We screened methylation in populations from Kenya and Florida to determine if methylation varied among populations, varied with introduction history (Kenyan invasion < 50 years old, Florida invasion ~150 years old), and could potentially compensate for decrease genetic variation with introductions. While recent literature has speculated on the importance of epigenetic effects for biological invasions, this is the first such study among wild vertebrates. Methylation was more frequent in Nairobi, and outlier loci suggest that populations may be differentiated. Methylation diversity was similar between populations, in spite of known lower genetic diversity in Nairobi, which suggests that epigenetic variation may compensate for decreased genetic diversity as a source of phenotypic variation during introduction. Our results suggest that methylation differences may be common among house sparrows, but research is needed to discern whether methylation impacts phenotypic variation.

Distribution Of Genes And Repetitive Elements In The Diabrotica Virgifera Virgifera Genome Estimated Using Bac Sequencing, Brad S. Coates, Analiza P. Alves, Haichuan Wang, Kimberly K. O. Walden, B. Wade French, Nicholas J. Miller, Craig A. Abel, Hugh M. Robertson, Thomas W. Sappington, Blair D. Siegfried

Department of Entomology: Faculty Publications

Feeding damage caused by the western corn rootworm, Diabrotica virgifera virgifera, is destructive to corn plants in North America and Europe where control remains challenging due to evolution of resistance to chemical and transgenic toxins. A BAC library, DvvBAC1, containing 109,486 clones with 104 ± 34.5 kb inserts was created, which has an ~4.56X genome coverage based upon a 2.58 Gb (2.80 pg) flow cytometry-estimated haploid genome size. Paired end sequencing of 1037 BAC inserts produced 1.17Mb of data (~0.05% genome coverage) and indicated ~9.4 and 16.0% of reads encode, respectively, endogenous genes and transposable elements (TEs). …

Triticum Mosaic Poacevirus Enlists P1 Rather Than Hc-Pro To Suppress Rna Silencing-Mediated Host Defense, Satyanarayana Tatineni, Feng Qu, Ruhui Li, Thomas Jack Morris, Roy French

Nebraska Center for Virology: Faculty Publications

Triticum mosaic virus (TriMV) is the type species of the newly established Poacevirus genus in the family Potyviridae. In this study, we demonstrate that in contrast to the helper component- proteinase (HC-Pro) of Potyvirus species, the P1 proteins of TriMV and Sugarcane steak mosaic poacevirus function in suppression of RNA silencing (SRS). TriMV P1 effectively suppressed silencing induced by single- or double-stranded RNAs (ss/ds RNAs), and disrupted the systemic spread of silencing signals at a step after silencing signal production. Interestingly, contrary to enhanced SRS activity of potyviral HC-Pro by co-expression with P1, the presence of TriMV HC-Pro reduced …

Identification Of Molecular Determinants From Moloney Leukemia Virus 10 Homolog (Mov10) Protein For Virion Packaging And Anti-Hiv-1 Activity, Aierken Abudu, Xiaojun Wang, Ying Dang, Tao Zhou, Shi-Hua Xiang, Yong -Hui Zheng

Nebraska Center for Virology: Faculty Publications

Background: MOV₁₀ inhibits HIV-1 replication after being packaged.

Results: A Gag binding plus all but one of seven helicase domains are required for MOV^₁₀ packaging. Nearly all residues are required for anti-HIV-1 activity. Conclusion: Gag binding is not sufficient for MOV₁₀ packaging, and multiple discontinuous domains regulate MOV₁₀ activity.

Significance: These findings uncover a new packaging mechanism and provide new insights into MOV₁₀ antiviral activity.

Case Study: In Situ Determination Of Protein Digestibility Of Dried Distillers Grains Containing 3 Lipid Concentrations Using A Mobile Bag Method, B. E. Meyer, C. L. Bouma, James C. Macdonald

Department of Animal Science: Faculty Publications

Ethanol producers remove lipid from distillers grains (DG) for applications such as biodiesel production. The effects of the lipid removal on ruminal protein degradability and total-tract CP digestibility of DG are not known. Five ruminally and duodenally cannulated Angus-cross steers (BW = 434 ± 15 kg) were used to incubate in situ bags for determination of protein digestibility of low-lipid (5.54%) DG, medium-lipid (8.40%) DG, high-lipid (12.46%) DG, and cottonseed meal. Ingredients were weighed into individual in situ bags and incubated in the ventral sac of the rumen for 16 h. After ruminal incubation and simulated abomasal digestion, bags were …

Technical Note: Estimating Beef-Cattle Forage Demand: Evaluating The Animal Unit Concept, T. L. Meyer, L. A. Stalker, J. D. Volesky, D. C. Adams, R. N. Funston, T. J. Klopfenstein, Walter H. Schacht

Department of Animal Science: Faculty Publications

The objective of this experiment was to evaluate the effect of BW and physiological status of a beef animal on forage intake. The experiment was repeated over 2 yr with 6 replications of 3 treatments per year: cow-calf pair (CCP, BW = 629 kg), nonlactating cow (NLC, BW = 503 kg), and yearling steer (YS, BW = 305 kg). The CCP was treated as one unit, with the sum of cow BW and calf BW comprising CCP BW. Calves averaged 42 d of age and 73 kg at the start of the experiment each year. Animals were housed in individual …

Estimation Of Breed-Specific Heterosis Effects For Birth, Weaning And Yearling Weight In Cattle., L. N. Schiermiester, R. M. Thallman, L. A. Kuehn, M. L. Spangler

Department of Animal Science: Faculty Publications

Heterosis, assumed proportional to expected breed heterozygosity, was calculated for 4,835 individuals with birth, weaning and yearling weight records from Cycle VII of the U.S. Meat Animal Research Center Germplasm Evaluation Program. Heterosis was further estimated by proportions of British x British (BxB), British x Continental (BxC) and Continental x Continental (CxC) crosses. Angus and Red Angus were considered a single breed for estimation of heterosis. Direct heritability estimates (SE) for birth, weaning and yearling weight were 0.39 (0.05), 0.18 (0.04) and .40 (0.06), respectively. The BxB covariate was significant and BxC approached significance for weaning weight. The BxB proportion …

Calving Date And Wintering System Effects On Cow And Calf Performance I: A Systems Approach To Beef Production In The Nebraska Sandhills, W. A. Griffin, L. A. Stalker, D. C. Adams, R. N. Funston, T. J. Klopfenstein

Department of Animal Science: Faculty Publications

A 4-yr study using 217 cows/yr (3/4 Red Angus, 1/4 Simmental) evaluated effects of calving date and wintering system on cow and calf performance from birth to harvest. Cows were assigned to 1 of 5 treatments: 1) March (Mar) calving cows wintered on native range, 2) Mar calving cows wintered on corn residue, 3) June (Jun) calving cows wintered on native range, 4) Jun calving cows wintered on corn residue, and 5) August (Aug) calving cows wintered on corn residue. Steers born in Mar entered the feedlot at weaning (calf-fed). Steers and heifers born in Jun and Aug were divided …

Smooth Bromegrass Pasture Beef Growing Systems: Fertilization Strategies And Economic Analysis, A. K. Watson, T. J. Klopfenstein, Walter H. Schacht, G. E. Erickson, D. R. Mark, Matt K. Luebbe, K. R. Brink, Matthew A. Greenquist

Department of Animal Science: Faculty Publications

In recent years, prices for N fertilizer have increased dramatically, reducing net returns of fertilized pasture systems. A 5-yr study from 2005 to 2009 was conducted to evaluate management strategies and relative differences in profitability for 3 methods of backgrounding calves on smooth bromegrass pastures. Forty-five steers were used each year for a total of 225 animals in a randomized complete block design. Treatments included pastures fertilized in the spring with 90 kg N/ha (FERT), nonfertilized pastures with calves supplemented daily with dried distillers grains plus solubles (DDGS) at 0.6% of BW (SUPP), and control (CONT) pastures that had no …

Widespread Triploidy In Western North American Aspen (Populus Tremuloides), Karen E. Mock, Colin M. Callahan, M. Nurul Islam-Faridi, John D. Shaw, Hardeep S. Rai, Stewart C. Sanderson, Carol A. Rowe, Ronald J. Ryel, Michael D. Madritch, Richard S. Gardner, Paul G. Wolf

Aspen Bibliography

No abstract provided.

Harvest Date Influence On Dry Matter Yield And Moisture Of Corn And Stover, Haibo Huang, Dan B. Faulkner, Larry L. Berger, Steven R. Eckhoff

Department of Animal Science: Faculty Publications

Harvest date greatly affects the biomass yield, moisture, and quality of corn and stover. Traditionally, corn and stover have been harvested at lower moisture levels. However, corn stover and grain can be more effectively utilized as animal feed and biomass-ethanol feedstock if they are collected before in-field dry down. This study determined dry matter yield, moisture content, and quality of corn and stover before, during, and after grain maturity in central Illinois. The two-year average kernel moisture was 37.4% (w.b.) when reaching physiological maturity. At the same time, the average stover moisture was 67.7% (w.b.). The dry matter yield of …

The Balance Of Proangiogenic And Antiangiogenic Vegfa Isoforms Regulate Follicle Development, Renee M. Mcfee, Timonthy G. Clopton, Andrea S. Cupp

Department of Animal Science: Faculty Publications

Vascular endothelial growth factor A (VEGFA) has been extensively studied because of its role in follicular development and is a principal angiogenic factor essential for angiogenesis. Since vascularization of the theca layer increases as follicles progress in size through preantral and antral stages, VEGFA might influence follicle growth via the regulation of angiogenesis. However, VEGFA might also influence follicular development through nonangiogenicmechanisms, since its expression has been localized in nonvascular follicles and cells. Alternative mRNA splicing of eight exons from the VEGFA gene results in the formation of various VEGFA isoforms. Each isoform has unique properties and is identified by …

Design Of A Distributed Hadoop Solution For The Multiple Sequence Alignment Algorithm: Clustal Omega, Jurate Daugelaite

Theses

Multiple Sequence Alignment (MSA) of DNA and protein sequences is one of the most essential techniques in the fields of molecular biology, computational biology and bioinformatics. It aids the identification and prediction of three dimensional structures, primary functions and evolutionary relatedness amongst groups of species, organisms, and genes. Since as the completion of the Human Genome Project and with the advent of sequencing initiatives such as the Genome 10K project, the rate of genome sequencing has increased exponentially, producing vast amounts of DNA and protein sequences. MSA algorithms, when applied to such sequence data, can identify common homology, structure and …