Gapped consensus motif discovery: evaluation of a new algorithm based on local multiple alignments and a sampling strategy

We check the efficiency and faisability of a novel method designed for the discovery of a priori unknown motifs described as gaps alternating with specific regions. Such motifs are searched for as consensi of non homologous biological sequences. The only specifications required concern the maximal gap length, the minimal frequency for specific characters and the minimal percentage (quorum) of sequences sharing the motif. Our method is based on a cooperation between a multiple alignment method for a quick detection of local similarities and a sampling strategy running candidate position specific scoring matrices to convergence. This rather original way implemented for converging to the solution proves efficient both on simulated data, gapped instances of the so-called challenge problem, promoter sites in Dicot plants and transcription factor binding sites in E.Coli. Our algorithm compares favorably with the MEME and STARS approaches in terms of accuracy

Motif Discovery with Compact Approaches - Design and Applications

In the post-genomic era, the ability to predict the behavior, the function, or the structure of biological entities, as well as interactions among them, plays a fundamental role in the discovery of information to help biologists to explain biological mechanisms. In this context, appropriate characterization of the structures under analysis, and the exploitation of combinatorial properties of sequences, are crucial steps towards the development of efficient algorithms and data structures to be able to perform the analysis of biological sequences. Similarity is a fundamental concept in Biology. Several functional and structural properties, and evolutionary mechanisms, can be predicted comparing new elements with already classified elements, or comparing elements with a similar structure of function to infer the common mechanism that is at the basis of the observed similar behavior. Such elements are commonly called motifs. Comparison-based methods for sequence analysis find their application in several biological contexts, such as identification of transcription factor binding sites, finding structural and functional similarities in proteins, and phylogeny. Therefore the development of adequate methodologies for motif discovery is of paramount interests for several fields in computational biology. In motif discovery in biosequences, it is common to assume that statistically significant candidates are those that are likely to hide some biologically significant property. For this purpose all the possible candidates are ranked according to some statistics on words (frequency, over/under representation, etc.). Then they are presented in output for further inspection by a biologist, who identifies the most promising subsequences, and tests them in laboratory to confirm their biological significance. Therefore, when designing algorithms for motif discovery, besides obviously aim at time and space efficiency, particular attention should be devoted to the output representation. In fact, even considering fixed length strings, the size of the candidate set become exponential if exhaustive enumeration is applied. This is already true when only exact matches are considered as candidate occurrences, and worsen if some kind of variability (for example a fixed number of mismatches is allowed). Alternatively, heuristics could be used, however without the warranty of finding the optimal solution. Computational power of nowadays computers can partially reduce these effects, in particular for short length candidates. However, if the size of the output is too big to be analyzed by human inspection the risk is to provide biologists with very fast, but useless tools. A possible solution relies on compact approaches. Compact approaches are based on the partition of the search space into classes. The classes must be designed in such a way that the score used to rank the candidates has a monotone behavior within each class. This allows the identification of a representative of each class, which is the element with the highest score. Consequently, it suffices to compute, and report in output, the score only for the representatives. In fact, we are guaranteed that for each element that has not been ranked there is another one (the representative of the class it belongs to) that is at least equally significant. The final user can then be presented with an output that has the size of the partition, rather than the size of the candidate space, with obvious advantages for the human-based analysis that follows the computer-based filtering of the pattern discovery algorithm. Compact approaches find applications both in searching and discovery frameworks. They can also be applied to several motif models: exact patterns, patterns with given mismatch distribution, patterns with unknown mismatch distribution, profiles (i.e. matrices), and under both i.i.d. and Markov distributions. The purpose of this chapter is to describe the basis of compact approaches, to provide the readers with the conceptual tools for applying compact approaches to the design of their algorithm for biosequence analysis. Moreover, examples of compact approaches that have been successfully developed for several motif models (e.g. exact words, co-occurrences, words with mismatches, etc) will be explained, and experimental results to discuss their power will be presented

Motif discovery in sequential data

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 2006.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.Includes bibliographical references (v. 2, leaves [435]-467).In this thesis, I discuss the application and development of methods for the automated discovery of motifs in sequential data. These data include DNA sequences, protein sequences, and real-valued sequential data such as protein structures and timeseries of arbitrary dimension. As more genomes are sequenced and annotated, the need for automated, computational methods for analyzing biological data is increasing rapidly. In broad terms, the goal of this thesis is to treat sequential data sets as unknown languages and to develop tools for interpreting an understanding these languages. The first chapter of this thesis is an introduction to the fundamentals of motif discovery, which establishes a common mode of thought and vocabulary for the subsequent chapters. One of the central themes of this work is the use of grammatical models, which are more commonly associated with the field of computational linguistics. In the second chapter, I use grammatical models to design novel antimicrobial peptides (AmPs). AmPs are small proteins used by the innate immune system to combat bacterial infection in multicellular eukaryotes. There is mounting evidence that these peptides are less susceptible to bacterial resistance than traditional antibiotics and may form the basis for a novel class of therapeutics.(cont.) In this thesis, I described the rational design of novel AmPs that show limited homology to naturally-occurring proteins but have strong bacteriostatic activity against several species of bacteria, including Staphylococcus aureus and Bacillus anthracis. These peptides were designed using a linguistic model of natural AmPs by treating the amino acid sequences of natural AmPs as a formal language and building a set of regular grammars to describe this language. is set of grammars was used to create novel, unnatural AmP sequences that conform to the formal syntax of natural antimicrobial peptides but populate a previously unexplored region of protein sequence space. The third chapter describes a novel, GEneric MOtif DIscovery Algorithm (Gemoda) for sequential data. Gemoda can be applied to any dataset with a sequential character, including both categorical and real-valued data. As I show, Gemoda deterministically discovers motifs that are maximal in composition and length. As well, the algorithm allows any choice of similarity metric for finding motifs. These motifs are representation-agnostic: they can be represented using regular expressions, position weight matrices, or any other model for sequential data.(cont.) I demonstrate a number of applications of the algorithm, including the discovery of motifs in amino acids and DNA sequences, and the discovery of conserved protein sub-structures. The final chapter is devoted to a series of smaller projects, employing tool methods indirectly related to motif discovery in sequential data. I describe the construction of a software tool, Biogrep that is designed to match large pattern sets against large biosequence databases in a parallel fashion. is makes biogrep well-suited to annotating sets of sequences using biologically significant patterns. In addition, I show that the BLOSUM series of amino acid substitution matrices, which are commonly used in motif discovery and sequence alignment problems, have changed drastically over time.The fidelity of amino acid sequence alignment and motif discovery tools depends strongly on the target frequencies implied by these underlying matrices. us, these results suggest that further optimization of these matrices is possible. The final chapter also contains two projects wherein I apply statistical motif discovery tools instead of grammatical tools.(cont.) In the first of these two, I develop three different physiochemical representations for a set of roughly 700 HIV-I protease substrates and use these representations for sequence classification and annotation. In the second of these two projects, I develop a simple statistical method for parsing out the phenotypic contribution of a single mutation from libraries of functional diversity that contain a multitude of mutations and varied phenotypes. I show that this new method successfully elucidates the effects of single nucleotide polymorphisms on the strength of a promoter placed upstream of a reporter gene. The central theme, present throughout this work, is the development and application of novel approaches to finding motifs in sequential data. The work on the design of AmPs is very applied and relies heavily on existing literature. In contrast, the work on Gemoda is the greatest contribution of this thesis and contains many new ideas.by Kyle L. Jensen.Ph.D

Querying Large Collections of Semistructured Data

An increasing amount of data is published as semistructured documents formatted with presentational markup. Examples include data objects such as mathematical expressions encoded with MathML or web pages encoded with XHTML. Our intention is to improve the state of the art in retrieving, manipulating, or mining such data. We focus first on mathematics retrieval, which is appealing in various domains, such as education, digital libraries, engineering, patent documents, and medical sciences. Capturing the similarity of mathematical expressions also greatly enhances document classification in such domains. Unlike text retrieval, where keywords carry enough semantics to distinguish text documents and rank them, math symbols do not contain much semantic information on their own. Unfortunately, considering the structure of mathematical expressions to calculate relevance scores of documents results in ranking algorithms that are computationally more expensive than the typical ranking algorithms employed for text documents. As a result, current math retrieval systems either limit themselves to exact matches, or they ignore the structure completely; they sacrifice either recall or precision for efficiency. We propose instead an efficient end-to-end math retrieval system based on a structural similarity ranking algorithm. We describe novel optimization techniques to reduce the index size and the query processing time. Thus, with the proposed optimizations, mathematical contents can be fully exploited to rank documents in response to mathematical queries. We demonstrate the effectiveness and the efficiency of our solution experimentally, using a special-purpose testbed that we developed for evaluating math retrieval systems. We finally extend our retrieval system to accommodate rich queries that consist of combinations of math expressions and textual keywords. As a second focal point, we address the problem of recognizing structural repetitions in typical web documents. Most web pages use presentational markup standards, in which the tags control the formatting of documents rather than semantically describing their contents. Hence, their structures typically contain more irregularities than descriptive (data-oriented) markup languages. Even though applications would greatly benefit from a grammar inference algorithm that captures structure to make it explicit, the existing algorithms for XML schema inference, which target data-oriented markup, are ineffective in inferring grammars for web documents with presentational markup. There is currently no general-purpose grammar inference framework that can handle irregularities commonly found in web documents and that can operate with only a few examples. Although inferring grammars for individual web pages has been partially addressed by data extraction tools, the existing solutions rely on simplifying assumptions that limit their application. Hence, we describe a principled approach to the problem by defining a class of grammars that can be inferred from very small sample sets and can capture the structure of most web documents. The effectiveness of this approach, together with a comparison against various classes of grammars including DTDs and XSDs, is demonstrated through extensive experiments on web documents. We finally use the proposed grammar inference framework to extend our math retrieval system and to optimize it further

On the Origin of Phenotypic Variation: Novel Technologies to Dissect Molecular Determinants of Phenotype

This thesis describes the conception, design, and development of novel computational tools, theoretical models, and experimental techniques applied to the dissection of molecular factors underlying phenotypic variation. The first part of my work is focused on finding rare genetic variants in pooled DNA samples, leading to the development of a novel set of algorithms, SNPseeker and SPLINTER, applied to next-generation sequencing data. The second part of my work describes the creation of a reporter system for DNA methylation for the purpose of dissecting the genetic contribution of tissue-specific patterns of DNA methylation across the genome. Finally the last part of my work is focused on understanding the basis of stochastic variation in gene expression with a focus on modeling and dissecting the relationship between single-cell protein variance and mean at a genome-wide scale

A Machine Learning Enhanced Scheme for Intelligent Network Management

The versatile networking services bring about huge influence on daily living styles while the amount and diversity of services cause high complexity of network systems. The network scale and complexity grow with the increasing infrastructure apparatuses, networking function, networking slices, and underlying architecture evolution. The conventional way is manual administration to maintain the large and complex platform, which makes effective and insightful management troublesome. A feasible and promising scheme is to extract insightful information from largely produced network data. The goal of this thesis is to use learning-based algorithms inspired by machine learning communities to discover valuable knowledge from substantial network data, which directly promotes intelligent management and maintenance. In the thesis, the management and maintenance focus on two schemes: network anomalies detection and root causes localization; critical traffic resource control and optimization. Firstly, the abundant network data wrap up informative messages but its heterogeneity and perplexity make diagnosis challenging. For unstructured logs, abstract and formatted log templates are extracted to regulate log records. An in-depth analysis framework based on heterogeneous data is proposed in order to detect the occurrence of faults and anomalies. It employs representation learning methods to map unstructured data into numerical features, and fuses the extracted feature for network anomaly and fault detection. The representation learning makes use of word2vec-based embedding technologies for semantic expression. Next, the fault and anomaly detection solely unveils the occurrence of events while failing to figure out the root causes for useful administration so that the fault localization opens a gate to narrow down the source of systematic anomalies. The extracted features are formed as the anomaly degree coupled with an importance ranking method to highlight the locations of anomalies in network systems. Two types of ranking modes are instantiated by PageRank and operation errors for jointly highlighting latent issue of locations. Besides the fault and anomaly detection, network traffic engineering deals with network communication and computation resource to optimize data traffic transferring efficiency. Especially when network traffic are constrained with communication conditions, a pro-active path planning scheme is helpful for efficient traffic controlling actions. Then a learning-based traffic planning algorithm is proposed based on sequence-to-sequence model to discover hidden reasonable paths from abundant traffic history data over the Software Defined Network architecture. Finally, traffic engineering merely based on empirical data is likely to result in stale and sub-optimal solutions, even ending up with worse situations. A resilient mechanism is required to adapt network flows based on context into a dynamic environment. Thus, a reinforcement learning-based scheme is put forward for dynamic data forwarding considering network resource status, which explicitly presents a promising performance improvement. In the end, the proposed anomaly processing framework strengthens the analysis and diagnosis for network system administrators through synthesized fault detection and root cause localization. The learning-based traffic engineering stimulates networking flow management via experienced data and further shows a promising direction of flexible traffic adjustment for ever-changing environments

The diversity and distribution of multihost viruses in bumblebees

The bumblebees (genus Bombus) are an ecologically and economically important group in decline. Their decline is driven by many factors, but parasites are believed to play a role. This thesis examines the factors that influence the diversity and distribution of multihost viruses in bumblebees using molecular and modelling techniques. In Chapter 2, I performed viral discovery to isolate new multihost viruses in bumblebees. I investigated factors that explain prevalence differences between different host species using co-phylogenetic models. I found that related hosts are infected with similar viral assemblages, related viruses infect similar host assemblages and related hosts are on average infected with related viruses. Chapter 3 investigated the ecology of four of the novel viruses in greater detail. I applied a multivariate probit regression to investigate the abiotic factors that may drive infection. I found that precipitation may have a positive or negative effect depending on the virus. Also, we observe a strong non-random association between two of the viruses. The novel viruses have considerably more diversity than the previously known viruses. Chapter 4 investigated the effect of pesticides on viral and non-viral infection. I exposed Bombus terrestris colonies to field realistic doses of the neoticotinoid pesticide clothianidin in the laboratory, to the mimic pulsed exposure of crop blooms. I found some evidence for a positive effect of uncertain size on the infection rate of pesticide exposed colonies relative to non-pesticide exposed colonies, a potentially important result. Chapter 5 explored the evolution of avirulent multihost digital organisms across fluctuating fitness landscapes within a discrete sequence space. Consistent with theory, I found that evolution across a fluctuating discrete landscape leads to a faster rate of adaptation, greater diversity and greater specialism or generalism, depending on the correlation between the landscapes. A large range of factors are found to be important in the distribution of infection and diversity of viruses, and we find evidence for abiotic, biotic and anthropogenic factors all playing a role.BBSR

IMPROVING BWA-MEM WITH GPU PARALLEL COMPUTING

Due to the many advances made in designing algorithms, especially the ones used in bioinformatics, it is becoming harder and harder to improve their efficiencies. Therefore, hardware acceleration using General-Purpose computing on Graphics Processing Unit has become a popular choice. BWA-MEM is an important part of the BWA software package for sequence mapping. Because of its high speed and accuracy, we choose to parallelize the popular short DNA sequence mapper. BWA has been a prevalent single node tool in genome alignment, and it has been widely studied for acceleration for a long time since the first version of the BWA package came out. This thesis presents the Big Data GPGPU distributed BWA-MEM, a tool that combines GPGPU acceleration and distributed computing. The four hardware parallelization techniques used are CPU multi-threading, GPU paralleled, CPU distributed, and GPU distributed. The GPGPU distributed software typically outperforms other parallelization versions. The alignment is performed on a distributed network, and each node in the network executes a separate GPGPU paralleled version of the software. We parallelize the chain2aln function in three levels. In Level 1, the function ksw\_extend2, an algorithm based on Smith-Waterman, is parallelized to handle extension on one side of the seed. In Level 2, the function chain2aln is parallelized to handle chain extension, where all seeds within the same chain are extended. In Level 3, part of the function mem\_align1\_core is parallelized for extending multiple chains. Due to the program's complexity, the parallelization work was limited at the GPU version of ksw\_extend2 parallelization Level 3. However, we have successfully combined Spark with BWA-MEM and ksw\_extend2 at parallelization Level 1, which has shown that the proposed framework is possible. The paralleled Level 3 GPU version of ksw\_extend2 demonstrated noticeable speed improvement with the test data set

Regulation of transcription factor binding specificity: from binding motifs to local DNA context

Regulation of transcription factor (TF) binding specificity lies at the heart of transcriptional control which governs how cells divide, differentiate, and respond to their environments. TFs are known to bind to DNA in a sequence specific manner, and such short sequence is known as transcription factor binding site (TFBS). However, the in vivo TF bound regions do not always contain a TFBS, and additionally, there are often excessive non-functional TFBSs with binding potential in the regulatory regions that are unbound for a given TF. This dissertation focuses on understanding the principles of TF binding specificity and is divided into two chapters: 1) developing a novel high throughput method that would facilitate the study of TF binding regulations and the resulting functional output; 2) analyzing the roles of local DNA context around TFBS in specifying TF localization. In the first chapter of this dissertation, we report a tool, Calling Cards Reporter Arrays (CCRA), that measures transcription factor (TF) binding and the consequences on gene expression for hundreds of synthetic promoters in yeast. Using Cbf1p and MAX, we demonstrate that the CCRA method is able to detect small changes in binding free energy with a sensitivity comparable to in vitro methods, enabling the measurement of energy landscapes in vivo. We then demonstrate the quantitative analysis of cooperative interactions by measuring Cbf1p binding at synthetic promoters with multiple sites. We find that the cooperativity between Cbf1p dimers varies sinusoidally with a period of 10.65 bp and energetic cost of 1.37 KBT for sites that are positioned “out of phase”. Finally, we characterize the binding and expression of a group of TFs, Tye7p, Gcr1p, and Gcr2p, that act together as a “TF collective”, an important but poorly characterized model of TF cooperativity. We demonstrate that Tye7p often binds promoters without its recognition site because it is recruited by other collective members, whereas these other members require their recognition sites, suggesting a hierarchy where these factors recruit Tye7p but not vice versa. Our experiments establish CCRA as a useful tool for quantitative investigations into TF binding and function. In the second chapter of this dissertation, we seek out to investigate if predictive information is embedded in local DNA context (LDC) on a large collection of TFs in Saccharomyces cerevisiae. We identify there is a general preference for TFs to bind at CG rich sequences; we then analyze whether such preference is linked to intrinsic nucleosome binding preference and found the CG preference in LDC for TF binding was independent of nucleosome regulation. We next examine the possible mechanism by which LDC influence TFs binding site selection, through recruiting ‘licensing’ factors or kinetically assisting TF search for a target site. We show high CG LDC is preferred by TFs in vitro condition, which suggests such preference only involves TFs and DNA and directs us to TF search kinetics mechanism. CG rich feature in LDC may act as an energetical funnel to facilitate TF recognizing a target binding site, and we verify the theoretical validity of this hypothesis with Gillespie simulation. In the end, we reveal CG preference was also present in a large group of human TFs, indicating the usage of LDC is a general mechanism for TF binding specificity