João Meidanis

On the consecutive ones property

Abstract A binary matrix has the Consecutive Ones Property (C1P) when there is a permutation of its rows that leaves the 1s consecutive in every column. We study the recognition problem for these matrices, giving a structure, PQR trees, generalizing the PQ trees of Booth and Lueker (1976). This new structure is capable of, not only recording all valid permutations when the matrix has the C1P, but also pointing out possible obstructions when the property does not hold. We recast the problem using collections of sets, developing a new theory for it. This problem appears naturally in several applications in molecular biology, for instance, in the construction of physical maps from hybridization data.

Reversal and transposition distance of linear chromosomes

In recent years we are seeing increasing interest in research on mutational events acting on large portions of chromosomes. Among these events, a reversal acts on a fragment of a chromosome, reversing the order and orientation of the genes, and a transposition moves fragments from one region to another within a chromosome. We analyze genomes evolving by reversals and transpositions. We present approximation algorithms to compute the reversal and transposition distance for linear permutations, and a lower bound on the reversal and transposition diameter of signed linear permutations.

Genome Sequence and Assembly of Bos indicus

Cattle are divided into 2 groups referred to as taurine and indicine, both of which have been under strong artificial selection due to their importance for human nutrition. A side effect of this domestication includes a loss of genetic diversity within each specialized breed. Recently, the first taurine genome was sequenced and assembled, allowing for a better understanding of this ruminant species. However, genetic information from indicine breeds has been limited. Here, we present the first genome sequence of an indicine breed (Nellore) generated with 52X coverage by SOLiD sequencing platform. As expected, both genomes share high similarity at the nucleotide level for all autosomes and the X chromosome. Regarding the Y chromosome, the homology was considerably lower, most likely due to uncompleted assembly of the taurine Y chromosome. We were also able to cover 97% of the annotated taurine protein-coding genes.

SCJ: A Breakpoint-Like Distance that Simplifies Several Rearrangement Problems

The breakpoint distance is one of the most straightforward genome comparison measures. Surprisingly, when it comes to defining it precisely for multichromosomal genomes with both linear and circular chromosomes, there is more than one way to go about it. Pevzner and Tesler gave a definition in a 2003 paper, Tannier et al. defined it differently in 2008, and in this paper we provide yet another alternative, calling it SCJ for single-cut-or-join, in analogy to the popular double cut and join (DCJ) measure. We show that several genome rearrangement problems, such as median and halving, become easy for SCJ, and provide linear and higher polynomial time algorithms for them. For the multichromosomal linear genome median problem, this is the first polynomial time algorithm described, since for other distances this problem is NP-hard. In addition, we show that small parsimony under SCJ is also easy, and can be solved by a variant of Fitchs algorithm. In contrast, big parsimony is NP-hard under SCJ. This new distance measure may be of value as a speedily computable, first approximation to distances based on more realistic rearrangement models.

A linear-time algorithm for proper interval graph recognition

Interval graphs are the intersection graphs of families of intervals in the real line. If the intervals can be chosen so that no interval contains another, we obtain the subclass of proper interval graphs. We show how to recognize proper interval graphs in linear time by constructing the clique partition from the output of a single lexicographic breadth-first search.

Whole-genome analysis of transporters in the plant pathogen Xylella fastidiosa.

SUMMARY The transport systems of the first completely sequenced genome of a plant parasite, Xylella fastidiosa, were analyzed. In all, 209 proteins were classified here as constitutive members of transport families; thus, we have identified 69 new transporters in addition to the 140 previously annotated. The analysis lead to several hints on potential ways of controlling the disease it causes on citrus trees. An ADP:ATP translocator, previously found in intracellular parasites only, was found in X. fastidiosa. A P-type ATPase is missing—among the 24 completely sequenced eubacteria to date, only three (including X. fastidiosa) do not have a P-type ATPase, and they are all parasites transmitted by insect vectors. An incomplete phosphotransferase system (PTS) was found, without the permease subunits—we conjecture either that they are among the hypothetical proteins or that the PTS plays a solely metabolic regulatory role. We propose that the Ttg2 ABC system might be an import system eventually involved in glutamate import rather than a toluene exporter, as previously annotated. X. fastidiosa exhibits fewer proteins with ≥4 α-helical transmembrane spanners than any other completely sequenced prokaryote to date. X. fastidiosa has only 2.7% of all open reading frames identifiable as major transporters, which puts it as the eubacterium having the lowest percentage of open reading frames involved in transport, closer to two archaea, Methanococcus jannaschii (2.4%) and Methanobacterium thermoautotrophicum (2.4%).

Sorting by Prefix Transpositions

A transposition is an operation that exchanges two consecutive, adjacent blocks in a permutation. A prefix transposition is a transposition that moves the first element in the permutation. In this work we present the first results on the problem of sorting permutations with the minimum number of prefix transpositions. This problem is a variation of the transposition distance problem, related to genome rearrangements. We present approximation algorithms with performance ratios of 2 and 3. We conjecture that the maximum prefix transposition distance is D(n) = n-?n/4? and present the results of several computational tests that support this. Finally, we propose an algorithm that decides whether a given permutation can be sorted using just the number of transpositions indicated by the breakpoint lower-bound.

AN ALTERNATIVE ALGEBRAIC FORMALISM FOR GENOME REARRANGEMENTS

Here we relate the recent theory of genome rearrangements to the theory of permutation groups in a new way and hope to set the ground for further advances in the area. This work was motivated by the fact that many arguments in genome rearrangements are of the form “look at the figure”, and lack more formal algebraic derivation. We intend to give the area a strong algebraic formalism, much as analytic geometry provided an alternative geometric arguments based on pictures.

Using workflow management in DNA sequencing

DNA fragment assembly is an area which makes intensive use of computers. However, computer users in this field are typically not experts in computer science, but build their working environment on an ad-hoc basis. In this situation, it seems appropriate to offer a kind of support which can contribute to a better organization of working environments, and a better exploitation of computer hardware and software. The authors describe an approach in this direction based on the emerging paradigms of workflow modeling and management. In particular they offer three contributions: first, they discuss why workflow management can be fruitfully adopted in DNA fragment assembly, and describe one way to perceive and model sequencing processes as workflows. Second, they outline an architecture of a system intended to support sequencing applications, whose core component is a workflow management system. Finally, they sketch their experience of building a prototype using commercial workflow management technology.

Genome rearrangements distance by fusion, fission, and transposition is easy

Given two genomes represented as circularly ordered sequences of genes, we show a polynomial time algorithm for the minimum weight series of fusion, jissions, and transpositions (with transpositions weighing twice as much as fusions and