Genome Halving with Double Cut and Join

Genome Halving with Double Cut and Join

10 Pages · 2007 · 174 KB · English

Introduction. In this paper we discuss a generalization of the genome halving process studied by El-Mabrouk.3 Before stating and solving the problem formally in the ensuing sections, we first give some motivation for the generalization. Models of genome rearrangement processes have permitted 

Genome Halving with Double Cut and Join free download


October 3, 2007 17:37 Proceedings Trim Size: 975in x 65in apbc057a GENOME HALVING WITH DOUBLE CUT AND JOIN ROBERT WARREN AND DAVID SANKOFF University of Ottawa The genome halving problem, previously solved by ElMabrouk for inversions and re ciprocal translocations, is here solved in a more general context allowing transpositions and block interchange as well, for genomes including multiple linear and circular chro mosomes We apply this to several data sets and compare the results to the previous algorithm 1 Introduction In this paper we discuss a generalization of the genome halving process studied by ElMabrouk 3 Before stating and solving the problem formally in the ensuing sections, we rst give some motivation for the generalization Models of genome rearrangement processes have permitted di erent repertoires of operations Certainly, realistic models must account for inversion Likewise, reciprocal translocations, Robertsonian translocations and other processes of chro mosome fusion and ssion, all of which involve transferring an entire telometric (ie, sux or pre x) region of at least one chromosome, are widespread across all eukaryotic domains Other movements of chromosomal fragments, usually not involving telomeres, are widely attested, and grouped together under the label of transpositions They are produced by a variety of processes, such as gene duplication followed by the loss of the original copy, or retrotransposition, or recombination errors Of the three true movement rearrangements, a inversion, translocation and trans position, only the rst two, separately or in combination, have proved very amenable to mathematical modeling, as exempli ed by the HannenhalliPevzner formula for the edit distance between two genomes, ie, the minimum number of operations required to transform one genome into another, and the ecient algorithm for pro ducing such a series of operations No formula or ecient algorithm exists for transposition, either by itself or in combination with the other two operations Recently, Yancopoulos et al6 introduced the \double cut and join" (DCJ) op eration as the basis for generating all the movement rearrangements This allowed for the inclusion of transposition with inversion and translocation in a single model a Duplications of genes or of chromosomal segments, as well as deletions and insertions are often considered as aspects of genome rearrangement, but they are not really of the same biological nature as the movements inherent in inversion, translocation and transposition, and mathematical models of rearrangement are not easily extended to encompass them 1 October 3, 2007 17:37 Proceedings Trim Size: 975in x 65in apbc057a 2 and resulted in a simpler formula for the edit distance and a simpler algorithm for recovering a corresponding series of operations A double cut and join operation simply cuts the chromosome in two places and joins the four ends of the cut in a new way The DCJ model, however, allows for the generation of a new kind of movement operation, a generalized transposition called block interchange, which is not repre sented in the biological genome rearrangement literature, though it has long been studied in the mathematical literature on rearrangement Both transposition and block interchange can be thought of as the excision of a fragment, its circularization, together counting as one DCJ operation, followed by a second set of cuts, where the circle is not necessarily cut in the same place it was originally created through a join, and then reincorporated at a new site in the chromosome Transpositions and block interchanges thus count as two DCJ operations whereas inversions and translocations each count as one The question arises, what is the biological signi cance of these chromosomal circles? On the evolutionary level, very little is known, but circular DNA structures abound in all sorts of organisms, even eukaryotes Circular chromosomes are well known in clinical studies 4 and the process of excision, circularization, linearization and reincorporation is exactly what happens in the con guration of the immune response in higher animals Because the evolutionary consequences of block inter change could have come about in other ways, there has been no reason to look for evidence of this process or even

------------- Read More -------------

Download genome-halving-with-double-cut-and-join.pdf

Genome Halving with Double Cut and Join related documents

DEPARTMENT of HEALTH and HUMAN - Centers for Disease Control and

507 Pages · 2008 · 6.61 MB · English

influenza, natural disasters, and terrorism, while remaining focused on the threats to health and local, tribal and territorial health network.

Immigration and Economy in the Globalization Process

236 Pages · 2002 · 1.63 MB · English

will need employees with the right skills and motivation. Switching to an active im- Finland by analyzing the development of the volume of foreign-born and foreign na- tionals and direct foreign . In the globalization trend of corporations, competition has shifted from natural re- source and expen

Addressing FRTB with Oracle Financial Services Analytical Applications

9 Pages · 2017 · 324 KB · English

Integrated risk and finance data model ensuring compliance with Risk Data Aggregation as per BCBS239 Identify 12-month stress period over observation time. » Default risk charge Oracle Financial Services Analytical Applications' (OFSAA) FRTB solution enables banks to accurately measure,.

Interpreting sloppy stick figures by graph rectification and

14 Pages · 2001 · 822 KB · English

1 Interpreting sloppy stick figures by graph rectification and constraint-based matching. James V. Mahoney and Markus P. J. Fromherz Xerox Palo Alto Research Center

Assistance and Accountability in Externally Managed Schools

37 Pages · 2008 · 263 KB · English

Edison Schools, Inc., is the largest and most visible among a growing number of. Education Management profit EMOs were managing 521 public schools serving nearly 240,000 students across the United . educational services; and management consulting under the “Edison Alliance” flag, through 

An integrated approach to product design and process selection

48 Pages · 2011 · 2.15 MB ·

Narayan Raman .. M? < Bs% .. a geometric series given by TEMP(y) = r * TEMP(

Normal Curve Equivalents and Percentiles

1 Pages · 2009 · 385 KB · English

Title: A.1-(28)_FINAL_Percentiles_NCEs_2009-08-23 Author: Dee McMann Created Date: 10/28/2009 3:50:39 PM

Rounding Algorithms for a Geometric Embedding of Minimum Multiway Cut

12 Pages · 2010 · 187 KB ·

between its embedded volume and minimum 3-way cut. and 5 we solve the 3-terminal case, giving matching up- cut of any embedded graph.

Afghanistan Floods and Landslide

12 Pages · 2014 · 585 KB · English

are Health and care (mobile health teams, psychosocial support and CBHFA), Water and Sanitation (distribution of .. health teams (MHTs, including deployment of teams across regions) working closely with CBHFA volunteers, psycho When operating, they erect a tent that serves as an OPD ward.

Word-Level Language Identification and Predicting Codeswitching Points in Swahili-English ...

9 Pages · 2016 · 136 KB · English

Proceedings of the Second Workshop on Computational Approaches to Code Switching, pages 21–29,. Austin, TX, November 1, 2016. cO2016 conveys meaning (Myers-Scotton, 1993b). A model should be able to see this Solorio and Liu look at English-Spanish codeswitching in a relatively small