MISSEL: a method to identify a large number of small species-specific genomic subsequences and its application to viruses classification

Continuous improvements in next generation sequencing technologies led to ever-increasing collections of genomic sequences, which have not been easily characterized by biologists, and whose analysis requires huge computational effort. The classification of species emerged as one of the main applications of DNA analysis and has been addressed with several approaches, e.g., multiple alignments-, phylogenetic trees-, statistical- and character-based methods

Effective transcription factor binding site prediction using a combination of optimization, a genetic algorithm and discriminant analysis to capture distant interactions

<p>Abstract</p> <p>Background</p> <p>Reliable transcription factor binding site (TFBS) prediction methods are essential for computer annotation of large amount of genome sequence data. However, current methods to predict TFBSs are hampered by the high false-positive rates that occur when only sequence conservation at the core binding-sites is considered.</p> <p>Results</p> <p>To improve this situation, we have quantified the performance of several Position Weight Matrix (PWM) algorithms, using exhaustive approaches to find their optimal length and position. We applied these approaches to bio-medically important TFBSs involved in the regulation of cell growth and proliferation as well as in inflammatory, immune, and antiviral responses (NF-κB, ISGF3, IRF1, STAT1), obesity and lipid metabolism (PPAR, SREBP, HNF4), regulation of the steroidogenic (SF-1) and cell cycle (E2F) genes expression. We have also gained extra specificity using a method, entitled SiteGA, which takes into account structural interactions within TFBS core and flanking regions, using a genetic algorithm (GA) with a discriminant function of locally positioned dinucleotide (LPD) frequencies.</p> <p>To ensure a higher confidence in our approach, we applied resampling-jackknife and bootstrap tests for the comparison, it appears that, optimized PWM and SiteGA have shown similar recognition performances. Then we applied SiteGA and optimized PWMs (both separately and together) to sequences in the Eukaryotic Promoter Database (EPD). The resulting SiteGA recognition models can now be used to search sequences for BSs using the web tool, SiteGA.</p> <p>Analysis of dependencies between close and distant LPDs revealed by SiteGA models has shown that the most significant correlations are between close LPDs, and are generally located in the core (footprint) region. A greater number of less significant correlations are mainly between distant LPDs, which spanned both core and flanking regions. When SiteGA and optimized PWM models were applied together, this substantially reduced false positives at least at higher stringencies.</p> <p>Conclusion</p> <p>Based on this analysis, SiteGA adds substantial specificity even to optimized PWMs and may be considered for large-scale genome analysis. It adds to the range of techniques available for TFBS prediction, and EPD analysis has led to a list of genes which appear to be regulated by the above TFs.</p

Protein fold recognition using genetic algorithm optimized voting scheme and profile bigram

In biology, identifying the tertiary structure of a protein helps determine its functions. A step towards tertiary structure identification is predicting a protein’s fold. Computational methods have been applied to determine a protein’s fold by assembling information from its structural, physicochemical and/or evolutionary properties. It has been shown that evolutionary information helps improve prediction accuracy. In this study, a scheme is proposed that uses the genetic algorithm (GA) to optimize a weighted voting scheme to improve protein fold recognition. This scheme incorporates k-separated bigram transition probabilities for feature extraction, which are based on the Position Specific Scoring Matrix (PSSM). A set of SVM classifiers are used for initial classification, whereupon their predictions are consolidated using the optimized weighted voting scheme. This scheme has been demonstrated on the Ding and Dubchak (DD), Extended Ding and Dubchak (EDD) and Taguchi and Gromhia (TG) datasets benchmarked data sets

Algorithms and tools for splicing junction donor recognition in genomic DNA sequences

The consensus sequences at splicing junctions in genomic DNA are required for pre-mRNA breaking and rejoining which must be carried out precisely. Programs currently available for identification or prediction of transcribed sequences from within genomic DNA are far from being powerful enough to elucidate genomic structure completely[4]. In this research, we develop a degenerate pattern match algorithm for 5\u27 splicing site (Donor Site) recognition.. Using the Motif models we developed, we can mine out the degenerate pattern information from the consensus splicing junction sequences. Our experimental results show that, this algorithm can correctly recognize 93% of the total donor sites at the right positions in the test DNA group. And more than 91% of the donor sites the algorithm predicted are correct. These precision rates are higher than the best existing donor classification algorithm[25]. This research made a very important progress toward our full gene structure detection algorithm development

Computational representation and discovery of transcription factor binding sites

Tesi per compendi de publicacions.The information about how, when, and where are produced the proteins has been one of the major challenge in molecular biology. The studies about the control of the gene expression are essential in order to have a better knowledge about the protein synthesis. The gene regulation is a highly controlled process that starts with the DNA transcription. This process operates at the gene level, hereditary basic units, which will be copied into primary ribonucleic acid (RNA). This first step is controlled by the binding of specific proteins, called as Transcription Factors (TF), with a sequence of the DNA (Deoxyribonucleic Acid) in the regulatory region of the gene. These DNA sequences are known as binding sites (BS). The binding sites motifs are usually very short (5 to 20 bp long) and highly degenerate. These sequences are expected to occur at random every few hundred base pairs. Besides, a TF can bind among different sites. Due to its highly variability, it is difficult to establish a consensus sequence. The study and identification binding sites is important to clarify the control of the gene expression. Due to the importance of identifying binding sites sequences, projects such as ENCODE (Encyclopedia of DNA elements), have dedicated efforts to map binding sites for large set of transcription factor to identify regulatory regions. In this thesis, we have approached the problem of the binding site detection from another angle. We have developed a set of toolkit for motif binding detection based on linear and non-linear models. First of all, we have been able to characterize binding sites using different approaches. The first one is based on the information that there is in each binding sites position. The second one is based on the covariance model of an aligned set of binding sites sequences. From these motif characterizations, we have proposed a new set of computational methods to detect binding sites. First, it was developed a new method based on parametric uncertainty measurement (Rényi entropy). This detection algorithm evaluates the variation on the total Rényi entropy of a set of sequences when a candidate sequence is assumed to be a true binding site belonging to the set. This method was found to perform especially well on transcription factors that the correlation among binding sites was null. The correlation among binding sites positions was considered through linear, Q-residuals, and non-linear models, alpha-Divergence and SIGMA. Q-residuals is a novel motif finding method which constructs a subspace based on the covariance of numerical DNA sequences. When the number of available sequences was small, The Q-residuals performance was significantly better and faster than all the others methodologies. Alpha-Divergence was based on the variation of the total parametric divergence in a set of aligned sequenced with binding evidence when a candidate sequence is added. Given an optimal q-value, the alpha-Divergence performance had a better behavior than the others methodologies in most of the studied transcription factor binding sites. And finally, a new computational tool, SIGMA, was developed as a trade-off between the good generalisation properties of pure entropy methods and the ability of position-dependency metrics to improve detection power. In approximately 70% of the cases considered, SIGMA exhibited better performance properties, at comparable levels of computational resources, than the methods which it was compared. This set of toolkits and the models for the detection of a set of transcription factor binding sites (TFBS) has been included in an R-package called MEET.La informació sobre com, quan i on es produeixen les proteïnes ha estat un dels majors reptes en la biologia molecular. Els estudis sobre el control de l'expressió gènica són essencials per conèixer millor el procés de síntesis d'una proteïna. La regulació gènica és un procés altament controlat que s'inicia amb la transcripció de l'ADN. En aquest procés, els gens, unitat bàsica d'herència, són copiats a àcid ribonucleic (RNA). El primer pas és controlat per la unió de proteïnes, anomenades factors de transcripció (TF), amb una seqüència d'ADN (àcid desoxiribonucleic) en la regió reguladora del gen. Aquestes seqüències s'anomenen punts d'unió i són específiques de cada proteïna. La unió dels factors de transcripció amb el seu corresponent punt d'unió és l'inici de la transcripció. Els punts d'unió són seqüències molt curtes (5 a 20 parells de bases de llargada) i altament degenerades. Aquestes seqüències poden succeir de forma aleatòria cada centenar de parells de bases. A més a més, un factor de transcripció pot unir-se a diferents punts. A conseqüència de l'alta variabilitat, és difícil establir una seqüència consensus. Per tant, l'estudi i la identificació del punts d'unió és important per entendre el control de l'expressió gènica. La importància d'identificar seqüències reguladores ha portat a projectes com l'ENCODE (Encyclopedia of DNA Elements) a dedicar grans esforços a mapejar les seqüències d'unió d'un gran conjunt de factors de transcripció per identificar regions reguladores. L'accés a seqüències genòmiques i els avanços en les tecnologies d'anàlisi de l'expressió gènica han permès també el desenvolupament dels mètodes computacionals per la recerca de motius. Gràcies aquests avenços, en els últims anys, un gran nombre de algorismes han sigut aplicats en la recerca de motius en organismes procariotes i eucariotes simples. Tot i la simplicitat dels organismes, l'índex de falsos positius és alt respecte als veritables positius. Per tant, per estudiar organismes més complexes és necessari mètodes amb més sensibilitat. En aquesta tesi ens hem apropat al problema de la detecció de les seqüències d'unió des de diferents angles. Concretament, hem desenvolupat un conjunt d'eines per la detecció de motius basats en models lineals i no-lineals. Les seqüències d'unió dels factors de transcripció han sigut caracteritzades mitjançant dues aproximacions. La primera està basada en la informació inherent continguda en cada posició de les seqüències d'unió. En canvi, la segona aproximació caracteritza la seqüència d'unió mitjançant un model de covariància. A partir d'ambdues caracteritzacions, hem proposat un nou conjunt de mètodes computacionals per la detecció de seqüències d'unió. Primer, es va desenvolupar un nou mètode basat en la mesura paramètrica de la incertesa (entropia de Rényi). Aquest algorisme de detecció avalua la variació total de l'entropia de Rényi d'un conjunt de seqüències d'unió quan una seqüència candidata és afegida al conjunt. Aquest mètode va obtenir un bon rendiment per aquells seqüències d'unió amb poca o nul.la correlació entre posicions. La correlació entre posicions fou considerada a través d'un model lineal, Qresiduals, i dos models no-lineals, alpha-Divergence i SIGMA. Q-residuals és una nova metodologia per la recerca de motius basada en la construcció d'un subespai a partir de la covariància de les seqüències d'ADN numèriques. Quan el nombre de seqüències disponible és petit, el rendiment de Q-residuals fou significant millor i més ràpid que en les metodologies comparades. Alpha-Divergence avalua la variació total de la divergència paramètrica en un conjunt de seqüències d'unió quan una seqüència candidata és afegida. Donat un q-valor òptim, alpha-Divergence va tenir un millor rendiment que les metodologies comparades en la majoria de seqüències d'unió dels factors de transcripció considerats. Finalment, un nou mètode computacional, SIGMA, va ser desenvolupat per tal millorar la potència de deteccióPostprint (published version

A cryptic RNA-binding domain mediates Syncrip recognition and exosomal partitioning of miRNA targets

Exosomal miRNA transfer is a mechanism for cell-cell communication that is important in the immune response, in the functioning of the nervous system and in cancer. Syncrip/hnRNPQ is a highly conserved RNA-binding protein that mediates the exosomal partition of a set of miRNAs. Here, we report that Syncrip's amino-terminal domain, which was previously thought to mediate protein-protein interactions, is a cryptic, conserved and sequence-specific RNA-binding domain, designated NURR (N-terminal unit for RNA recognition). The NURR domain mediates the specific recognition of a short hEXO sequence defining Syncrip exosomal miRNA targets, and is coupled by a non-canonical structural element to Syncrip's RRM domains to achieve high-affinity miRNA binding. As a consequence, Syncrip-mediated selection of the target miRNAs implies both recognition of the hEXO sequence by the NURR domain and binding of the RRM domains 5′ to this sequence. This structural arrangement enables Syncrip-mediated selection of miRNAs with different seed sequences. © 2018 The Author(s)

Application of amino acid occurrence for discriminating different folding types of globular proteins

<p>Abstract</p> <p>Background</p> <p>Predicting the three-dimensional structure of a protein from its amino acid sequence is a long-standing goal in computational/molecular biology. The discrimination of different structural classes and folding types are intermediate steps in protein structure prediction.</p> <p>Results</p> <p>In this work, we have proposed a method based on linear discriminant analysis (LDA) for discriminating 30 different folding types of globular proteins using amino acid occurrence. Our method was tested with a non-redundant set of 1612 proteins and it discriminated them with the accuracy of 38%, which is comparable to or better than other methods in the literature. A web server has been developed for discriminating the folding type of a query protein from its amino acid sequence and it is available at http://granular.com/PROLDA/.</p> <p>Conclusion</p> <p>Amino acid occurrence has been successfully used to discriminate different folding types of globular proteins. The discrimination accuracy obtained with amino acid occurrence is better than that obtained with amino acid composition and/or amino acid properties. In addition, the method is very fast to obtain the results.</p

Method of predicting Splice Sites based on signal interactions

BACKGROUND: Predicting and proper ranking of canonical splice sites (SSs) is a challenging problem in bioinformatics and machine learning communities. Any progress in SSs recognition will lead to better understanding of splicing mechanism. We introduce several new approaches of combining a priori knowledge for improved SS detection. First, we design our new Bayesian SS sensor based on oligonucleotide counting. To further enhance prediction quality, we applied our new de novo motif detection tool MHMMotif to intronic ends and exons. We combine elements found with sensor information using Naive Bayesian Network, as implemented in our new tool SpliceScan. RESULTS: According to our tests, the Bayesian sensor outperforms the contemporary Maximum Entropy sensor for 5' SS detection. We report a number of putative Exonic (ESE) and Intronic (ISE) Splicing Enhancers found by MHMMotif tool. T-test statistics on mouse/rat intronic alignments indicates, that detected elements are on average more conserved as compared to other oligos, which supports our assumption of their functional importance. The tool has been shown to outperform the SpliceView, GeneSplicer, NNSplice, Genio and NetUTR tools for the test set of human genes. SpliceScan outperforms all contemporary ab initio gene structural prediction tools on the set of 5' UTR gene fragments. CONCLUSION: Designed methods have many attractive properties, compared to existing approaches. Bayesian sensor, MHMMotif program and SpliceScan tools are freely available on our web site. REVIEWERS: This article was reviewed by Manyuan Long, Arcady Mushegian and Mikhail Gelfand

Computational analyses of eukaryotic promoters

Computational analysis of eukaryotic promoters is one of the most difficult problems in computational genomics and is essential for understanding gene expression profiles and reverse-engineering gene regulation network circuits. Here I give a basic introduction of the problem and recent update on both experimental and computational approaches. More details may be found in the extended references. This review is based on a summer lecture given at Max Planck Institute at Berlin in 2005