New Contig Creation Algorithm for the de novo DNA Assembly Problem

DNA assembly is among the most fundamental and difficult problems in bioinformatics. Near optimal assembly solutions are available for bacterial and small genomes, however assembling large and complex genomes especially the human genome using Next-Generation-Sequencing (NGS) technologies is shown to be very difficult because of the highly repetitive and complex nature of the human genome, short read lengths, uneven data coverage and tools that are not specifically built for human genomes. Moreover, many algorithms are not even scalable to human genome datasets containing hundreds of millions of short reads. The DNA assembly problem is usually divided into several subproblems including DNA data error detection and correction, contig creation, scaffolding and contigs orientation; each can be seen as a distinct research area. This thesis specifically focuses on creating contigs from the short reads and combining them with outputs from other tools in order to obtain better results. Three different assemblers including SOAPdenovo [Li09], Velvet [ZB08] and Meraculous [CHS+11] are selected for comparative purposes in this thesis. Obtained results show that this thesis’ work produces comparable results to other assemblers and combining our contigs to outputs from other tools, produces the best results outperforming all other investigated assemblers.

Perceived Deservingness and the Toleration of Human Rights Violations: The Problem and a Possible Solution

Despite general endorsement of universal human rights, people continue to tolerate specific human rights violations. I conducted a two-part study to investigate this issue. For Part I, I examined whether people tolerated torture (a human rights violation) based on the morality and deservingness of the target. Participants tolerated torture more when the target had committed a highly morally reprehensible transgression. This effect was mediated by the target’s perceived deservingness for harsh treatment, and held over and above participants’ abstract support for the right to humane treatment. For Part II, hypocrisy induction was used in an attempt to reduce participants’ toleration of the torture. Participants were assigned to either the hypocrisy induction or control condition. Unexpectedly, participants who tolerated the torture more in Part I reduced their toleration the most in the control condition, possibly because of consistency and floor effects. Limitations and implications of the findings are discussed.

Letter to Mr. Steers from Samuel D. Woodruff regarding Lot 30

Letter to Mr. Steers from Samuel D. Woodruff regarding Lot 30, Concession 2 in Enniskillen (1 double sided page). Mr. Woodruff is asking Mr. Steers to inform him if he will attest to the claim of Mr. Clement. This letter is written in pencil and is quite faded but the text is still legible, April 18, 1848.

Diagram of lot no. 10 in Willoughby

Diagram of lot no. 10 in Willoughby. The names on the outside of this document include: Matthew Singh, provincial land surveyor, Toronto; George S. Field, contractor, Niagara Falls; E. T. Phelps and H. Lyman, lawyer, Niagara Falls. The document is quite warn and fragile. This does not affect the text, n.d.

Diagram of Lot 142 and Lot 186 showing the line of the road in red

Diagram of Lot 142 and Lot 186 showing the line of the road in red, Dec.10, 1856.

Chart of station 2, crop sections of the old back ditch on the south side of the feeder, station 45, station 118 and the total length from the culvert to lot no. 5

Chart of station 2, crop sections of the old back ditch on the south side of the feeder, station 45, station 118 and the total length from the culvert to lot no. 5. This is signed by Fred Holmes, April 13, 1857.

List showing the quantity of excavation from lot no.5 to Marshville Culvert

List showing the quantity of excavation from lot no.5 to Marshville Culvert, n.d.

Calculation of ditching in the south side of the feeder from Brown’s ditch culvert to lot no.5

Calculation of ditching in the south side of the feeder from Brown’s ditch culvert to lot no.5, n.d.

Plan of levels of marsh land on the line of the proposed ditch from Lyons Creek Culvert on the Welland Canal to lot no. 32 in the 2nd concession of Wainfleet

Plan of levels of marsh land on the line of the proposed ditch from Lyons Creek Culvert on the Welland Canal to lot no. 32 in the 2nd concession of Wainfleet (1 page, hand drawn), n.d.

Map of measurements of lot no.186

Map of measurements of lot no.186, Dec. 19, 1855.

Certificate that Joseph Kingsmill, sheriff, has sold 5 acres in Lot no. 22 in the 7th Concession of Crowland to Joseph A. Woodruff

Certificate that Joseph Kingsmill, sheriff, has sold 5 acres in Lot no. 22 in the 7th Concession of Crowland to Joseph A. Woodruff, May 23, 1857.

Certificate that Joseph Kingsmill, sheriff, has sold 3 ½ acres in Lot no. 34 in the 3rd Concession of Wainfleet to W. H. Dickson

Certificate that Joseph Kingsmill, sheriff, has sold 3 ½ acres in Lot no. 34 in the 3rd Concession of Wainfleet to W. H. Dickson, May 23, 1857.

Certificate that Joseph Kingsmill, sheriff, has sold 3 acres in Lot no. 7 [?] in Grimsby to W. H. Dickson

Certificate that Joseph Kingsmill, sheriff, has sold 3 acres in Lot no. 7 [?] in Grimsby to W. H. Dickson, May 23, 1857.

Certificate that Joseph Kingsmill, sheriff, has sold 6 acres in Lot no. 9 in the 4th Concession of Caistor to W.H. Dickson [originally said S.D. Woodruff, but this was crossed out]

Certificate that Joseph Kingsmill, sheriff, has sold 6 acres in Lot no. 9 in the 4th Concession of Caistor to W.H. Dickson [originally said S.D. Woodruff, but this was crossed out], May 23, 1857.

Certificate that Joseph Kingsmill, sheriff, has sold 4 acres in Lot no. 18 in the 4th Concession of Humberland to W.H. Dickson

Certificate that Joseph Kingsmill, sheriff, has sold 4 acres in Lot no. 18 in the 4th Concession of Humberland to W.H. Dickson, May 23, 1857.