Quantitative modelling of transcription factor binding sites

Abstract One of the most important issues in molecular biology is to understand regulatory mechanisms that control gene expression. Gene expression is often regulated by proteins, called transcription factors which bind to short (5 to 20 base pairs),degenerate segments of DNA. Experimental efforts towards understanding the sequence specificity of transcription factors is laborious and expensive, but can be substantially accelerated with the use of computational predictions. This thesis describes the use of algorithms and resources for transcriptionfactor binding site analysis in addressing quantitative modelling, where probabilitic models are built to represent binding properties of a transcription factor and can be used to find new functional binding sites in genomes. Initially, an open-access database(HTPSELEX) was created, holding high quality binding sequences for two eukaryotic families of transcription factors namely CTF/NF1 and LEFT/TCF. The binding sequences were elucidated using a recently described experimental procedure called HTP-SELEX, that allows generation of large number (> 1000) of binding sites using mass sequencing technology. For each HTP-SELEX experiments we also provide accurate primary experimental information about the protein material used, details of the wet lab protocol, an archive of sequencing trace files, and assembled clone sequences of binding sequences. The database also offers reasonably large SELEX libraries obtained with conventional low-throughput protocols.The database is available at http://wwwisrec.isb-sib.ch/htpselex/ and and ftp://ftp.isrec.isb-sib.ch/pub/databases/htpselex. The Expectation-Maximisation(EM) algorithm is one the frequently used methods to estimate probabilistic models to represent the sequence specificity of transcription factors. We present computer simulations in order to estimate the precision of EM estimated models as a function of data set parameters(like length of initial sequences, number of initial sequences, percentage of nonbinding sequences). We observed a remarkable robustness of the EM algorithm with regard to length of training sequences and the degree of contamination. The HTPSELEX database and the benchmarked results of the EM algorithm formed part of the foundation for the subsequent project, where a statistical framework called hidden Markov model has been developed to represent sequence specificity of the transcription factors CTF/NF1 and LEF1/TCF using the HTP-SELEX experiment data. The hidden Markov model framework is capable of both predicting and classifying CTF/NF1 and LEF1/TCF binding sites. A covariance analysis of the binding sites revealed non-independent base preferences at different nucleotide positions, providing insight into the binding mechanism. We next tested the LEF1/TCF model by computing binding scores for a set of LEF1/TCF binding sequences for which relative affinities were determined experimentally using non-linear regression. The predicted and experimentally determined binding affinities were in good correlation.

Statistical Methods for Conservation and Alignment Quality in Proteins

Construction of multiple sequence alignments is a fundamental task in Bioinformatics. Multiple sequence alignments are used as a prerequisite in many Bioinformatics methods, and subsequently the quality of such methods can be critically dependent on the quality of the alignment. However, automatic construction of a multiple sequence alignment for a set of remotely related sequences does not always provide biologically relevant alignments.Therefore, there is a need for an objective approach for evaluating the quality of automatically aligned sequences. The profile hidden Markov model is a powerful approach in comparative genomics. In the profile hidden Markov model, the symbol probabilities are estimated at each conserved alignment position. This can increase the dimension of parameter space and cause an overfitting problem. These two research problems are both related to conservation. We have developed statistical measures for quantifying the conservation of multiple sequence alignments. Two types of methods are considered, those identifying conserved residues in an alignment position, and those calculating positional conservation scores. The positional conservation score was exploited in a statistical prediction model for assessing the quality of multiple sequence alignments. The residue conservation score was used as part of the emission probability estimation method proposed for profile hidden Markov models. The results of the predicted alignment quality score highly correlated with the correct alignment quality scores, indicating that our method is reliable for assessing the quality of any multiple sequence alignment. The comparison of the emission probability estimation method with the maximum likelihood method showed that the number of estimated parameters in the model was dramatically decreased, while the same level of accuracy was maintained. To conclude, we have shown that conservation can be successfully used in the statistical model for alignment quality assessment and in the estimation of emission probabilities in the profile hidden Markov models.

Speech Recognition of Malayalam Numbers

Digit speech recognition is important in many applications such as automatic data entry, PIN entry, voice dialing telephone, automated banking system, etc. This paper presents speaker independent speech recognition system for Malayalam digits. The system employs Mel frequency cepstrum coefficient (MFCC) as feature for signal processing and Hidden Markov model (HMM) for recognition. The system is trained with 21 male and female voices in the age group of 20 to 40 years and there was 98.5% word recognition accuracy (94.8% sentence recognition accuracy) on a test set of continuous digit recognition task.

Automated Transcription System for Malayalam Language

Malayalam is one of the 22 scheduled languages in India with more than 130 million speakers. This paper presents a report on the development of a speaker independent, continuous transcription system for Malayalam. The system employs Hidden Markov Model (HMM) for acoustic modeling and Mel Frequency Cepstral Coefficient (MFCC) for feature extraction. It is trained with 21 male and female speakers in the age group ranging from 20 to 40 years. The system obtained a word recognition accuracy of 87.4% and a sentence recognition accuracy of 84%, when tested with a set of continuous speech data.

Malayalam Isolated Digit Recognition using HMM and PLP cepstral coefficient

Development of Malayalam speech recognition system is in its infancy stage; although many works have been done in other Indian languages. In this paper we present the first work on speaker independent Malayalam isolated speech recognizer based on PLP (Perceptual Linear Predictive) Cepstral Coefficient and Hidden Markov Model (HMM). The performance of the developed system has been evaluated with different number of states of HMM (Hidden Markov Model). The system is trained with 21 male and female speakers in the age group ranging from 19 to 41 years. The system obtained an accuracy of 99.5% with the unseen data

Connected digit speech recognition system for Malayalam language

A connected digit speech recognition is important in many applications such as automated banking system, catalogue-dialing, automatic data entry, automated banking system, etc. This paper presents an optimum speaker-independent connected digit recognizer forMalayalam language. The system employs Perceptual Linear Predictive (PLP) cepstral coefficient for speech parameterization and continuous density Hidden Markov Model (HMM) in the recognition process. Viterbi algorithm is used for decoding. The training data base has the utterance of 21 speakers from the age group of 20 to 40 years and the sound is recorded in the normal office environment where each speaker is asked to read 20 set of continuous digits. The system obtained an accuracy of 99.5 % with the unseen data.

A Comparative study of HMM and SVM in Malayalam Digit Recognition

A primary medium for the human beings to communicate through language is Speech. Automatic Speech Recognition is wide spread today. Recognizing single digits is vital to a number of applications such as voice dialling of telephone numbers, automatic data entry, credit card entry, PIN (personal identification number) entry, entry of access codes for transactions, etc. In this paper we present a comparative study of SVM (Support Vector Machine) and HMM (Hidden Markov Model) to recognize and identify the digits used in Malayalam speech.

Modeling Stock Order Flows and Learning Market-Making from Data

Stock markets employ specialized traders, market-makers, designed to provide liquidity and volume to the market by constantly supplying both supply and demand. In this paper, we demonstrate a novel method for modeling the market as a dynamic system and a reinforcement learning algorithm that learns profitable market-making strategies when run on this model. The sequence of buys and sells for a particular stock, the order flow, we model as an Input-Output Hidden Markov Model fit to historical data. When combined with the dynamics of the order book, this creates a highly non-linear and difficult dynamic system. Our reinforcement learning algorithm, based on likelihood ratios, is run on this partially-observable environment. We demonstrate learning results for two separate real stocks.

A framework for monitoring and runtime recovery of web service-based applications

Service provisioning is a challenging research area for the design and implementation of autonomic service-oriented software systems. It includes automated QoS management for such systems and their applications. Monitoring, Diagnosis and Repair are three key features of QoS management. This work presents a self-healing Web service-based framework that manages QoS degradation at runtime. Our approach is based on proxies. Proxies act on meta-level communications and extend the HTTP envelope of the exchanged messages with QoS-related parameter values. QoS Data are filtered over time and analysed using statistical functions and the Hidden Markov Model. Detected QoS degradations are handled with proxies. We experienced our framework using an orchestrated electronic shop application (FoodShop).

Predição computacional de promotores em Xanthomonas axonopodis pv. citri

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Análise de técnicas de reconhecimento de padrões para a identificação biométrica de usuários em aplicações WEB Utilizando faces a partir de vídeos

Pós-graduação em Ciência da Computação - IBILCE

Desenvolvimento de recursos para a construção de um sistema texto-fala para o português brasileiro

Sistema Texto-Fala (TTS) é atualmente uma tecnologia madura que é utilizada em muitas aplicações. Alguns módulos de um sistema TTS são dependentes do idioma e, enquanto existem muitos recursos disponíveis para a língua inglesa, os recursos para alguns idiomas ainda são limitados. Este trabalho descreve o desenvolvimento de um sistema TTS completo para português brasileiro (PB), o qual também apresenta os recursos já disponíveis. O sistema usa a plataforma MARY e o processo de síntese da voz é baseado em cadeias escondidas de Markov (HMM). Algumas das contribuições deste trabalho consistem na implementação de silabação, determinação da sílaba tônica e conversão grafema-fonema (G2P). O trabalho também descreve as etapas para a organização dos recursos desenvolvidos e a criação de uma voz em PB junto ao MARY. Estes recursos estão disponíveis e facilita a pesquisa na normalização de texto e síntese baseada em HMM par o PB.

Ab initio protein folding simulations using atomic burials as informational intermediates between sequence and structure

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

A complex chromosomal rearrangement involving chromosomes 2, 5, and X in autism spectrum disorder

Here, we describe a female patient with autism spectrum disorder and dysmorphic features that harbors a complex genetic alteration, involving a de novo balanced translocation t(2;X)(q11;q24), a 5q11 segmental trisomy and a maternally inherited isodisomy on chromosome 5. All the possibly damaging genetic effects of such alterations are discussed. In light of recent findings on ASD genetic causes, the hypothesis that all these alterations might be acting in orchestration and contributing to the phenotype is also considered. (C) 2012 Wiley Periodicals, Inc.

Design and implementation of bioinformatics tools for large scale genome annotation

The continuous increase of genome sequencing projects produced a huge amount of data in the last 10 years: currently more than 600 prokaryotic and 80 eukaryotic genomes are fully sequenced and publically available. However the sole sequencing process of a genome is able to determine just raw nucleotide sequences. This is only the first step of the genome annotation process that will deal with the issue of assigning biological information to each sequence. The annotation process is done at each different level of the biological information processing mechanism, from DNA to protein, and cannot be accomplished only by in vitro analysis procedures resulting extremely expensive and time consuming when applied at a this large scale level. Thus, in silico methods need to be used to accomplish the task. The aim of this work was the implementation of predictive computational methods to allow a fast, reliable, and automated annotation of genomes and proteins starting from aminoacidic sequences. The first part of the work was focused on the implementation of a new machine learning based method for the prediction of the subcellular localization of soluble eukaryotic proteins. The method is called BaCelLo, and was developed in 2006. The main peculiarity of the method is to be independent from biases present in the training dataset, which causes the over‐prediction of the most represented examples in all the other available predictors developed so far. This important result was achieved by a modification, made by myself, to the standard Support Vector Machine (SVM) algorithm with the creation of the so called Balanced SVM. BaCelLo is able to predict the most important subcellular localizations in eukaryotic cells and three, kingdom‐specific, predictors were implemented. In two extensive comparisons, carried out in 2006 and 2008, BaCelLo reported to outperform all the currently available state‐of‐the‐art methods for this prediction task. BaCelLo was subsequently used to completely annotate 5 eukaryotic genomes, by integrating it in a pipeline of predictors developed at the Bologna Biocomputing group by Dr. Pier Luigi Martelli and Dr. Piero Fariselli. An online database, called eSLDB, was developed by integrating, for each aminoacidic sequence extracted from the genome, the predicted subcellular localization merged with experimental and similarity‐based annotations. In the second part of the work a new, machine learning based, method was implemented for the prediction of GPI‐anchored proteins. Basically the method is able to efficiently predict from the raw aminoacidic sequence both the presence of the GPI‐anchor (by means of an SVM), and the position in the sequence of the post‐translational modification event, the so called ω‐site (by means of an Hidden Markov Model (HMM)). The method is called GPIPE and reported to greatly enhance the prediction performances of GPI‐anchored proteins over all the previously developed methods. GPIPE was able to predict up to 88% of the experimentally annotated GPI‐anchored proteins by maintaining a rate of false positive prediction as low as 0.1%. GPIPE was used to completely annotate 81 eukaryotic genomes, and more than 15000 putative GPI‐anchored proteins were predicted, 561 of which are found in H. sapiens. In average 1% of a proteome is predicted as GPI‐anchored. A statistical analysis was performed onto the composition of the regions surrounding the ω‐site that allowed the definition of specific aminoacidic abundances in the different considered regions. Furthermore the hypothesis that compositional biases are present among the four major eukaryotic kingdoms, proposed in literature, was tested and rejected. All the developed predictors and databases are freely available at: BaCelLo http://gpcr.biocomp.unibo.it/bacello eSLDB http://gpcr.biocomp.unibo.it/esldb GPIPE http://gpcr.biocomp.unibo.it/gpipe