Computational pan-genomics: status, promises and challenges

International audienceMany disciplines, from human genetics and oncology to plant breeding, microbiology and virology, commonly face the challenge of analyzing rapidly increasing numbers of genomes. In case of Homo sapiens, the number of sequenced genomes will approach hundreds of thousands in the next few years. Simply scaling up established bioinformatics pipelines will not be sufficient for leveraging the full potential of such rich genomic data sets. Instead, novel, qualitatively different computational methods and paradigms are needed. We will witness the rapid extension of computational pan-genomics, a new sub-area of research in computational biology. In this article, we generalize existing definitions and understand a pan-genome as any collection of genomic sequences to be analyzed jointly or to be used as a reference. We examine already available approaches to construct and use pan-genomes, discuss the potential benefits of future technologies and methodologies and review open challenges from the vantage point of the above-mentioned biological disciplines. As a prominent example for a computational paradigm shift, we particularly highlight the transition from the representation of reference genomes as strings to representations as graphs. We outline how this and other challenges from different application domains translate into common computational problems, point out relevant bioinformatics techniques and identify open problems in computer science. With this review, we aim to increase awareness that a joint approach to computational pan-genomics can help address many of the problems currently faced in various domains

Letter: TreeAdder: a tool to assist the optimal positioning of a new leaf into an existing phylogenetic tree

TreeAdder is a computer application that adds a leaf in all possible positions on a phylogenetic tree. The resulting set of trees represent a dataset appropriate for maximum likelihood calculation of the optimal tree. TreeAdder therefore provides a utility for what was previously a tedious and error-prone process

Malicious cryptography techniques for unreversable (malicious or not) binaries

Fighting against computer malware require a mandatory step of reverse engineering. As soon as the code has been disassemblied/decompiled (including a dynamic analysis step), there is a hope to understand what the malware actually does and to implement a detection mean. This also applies to protection of software whenever one wishes to analyze them. In this paper, we show how to amour code in such a way that reserse engineering techniques (static and dymanic) are absolutely impossible by combining malicious cryptography techniques developped in our laboratory and new types of programming (k-ary codes). Suitable encryption algorithms combined with new cryptanalytic approaches to ease the protection of (malicious or not) binaries, enable to provide both total code armouring and large scale polymorphic features at the same time. A simple 400 Kb of executable code enables to produce a binary code and around $2^{140}$ mutated forms natively while going far beyond the old concept of decryptor.Comment: 17 pages, 2 figures, accepted for presentation at H2HC'1

Metamorphic Code Generation from LLVM IR Bytecode

Metamorphic software changes its internal structure across generations with its functionality remaining unchanged. Metamorphism has been employed by malware writers as a means of evading signature detection and other advanced detection strate- gies. However, code morphing also has potential security benefits, since it increases the “genetic diversity” of software. In this research, we have created a metamorphic code generator within the LLVM compiler framework. LLVM is a three-phase compiler that supports multiple source languages and target architectures. It uses a common intermediate representation (IR) bytecode in its optimizer. Consequently, any supported high-level programming language can be transformed to this IR bytecode as part of the LLVM compila- tion process. Our metamorphic generator functions at the IR bytecode level, which provides many advantages over previously developed metamorphic generators. The morphing techniques that we employ include dead code insertion—where the dead code is actually executed within the morphed code—and subroutine permutation. We have tested the effectiveness of our code morphing using hidden Markov model analysis