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A New Approach for Parameter Estimation in the sequence-structure alignment of Non-Coding RNAs

JOURNAL OF INFORMATION SCIENCE AND ENGINEERING 2015年第2期31卷 597-607页

作者： Song, Yinglei Chi, Albert Y. Jiangsu Univ Sci & Technol Sch Engn & Comp Sci Zhenjiang 212003 Jiangsu Peoples R China Univ Maryland Eastern Shore Dept Math & Comp Sci Princess Anne MD 21853 USA

Recently, searching genomes with a computer program has become an important approach for identifying new noncoding RNAs (ncRNA). Such a computer program often determines whether a sequence segment is the searched ncRNA or not by aligning the sequence segment to a secondary structure model for the searched ncRNA family. To a large extent, the search accuracy depends on the accuracy of the secondary structure model. In this paper, we develop a novel algorithm that can estimate the parameters associated with a few crucial structure features that have been proposed in previous work. This algorithm determines the relative importance of the crucial structure features by solving a convex optimization problem whose objective is to maximize the recognition ability of the structure model. Our experiments also show that this new parameter estimation algorithm can significantly improve the search accuracy.

关键词： non-coding RNA sequence-structure alignment parameter estimation convex optimization structure features

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Variable gap penalty for protein sequence-structure alignment

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PROTEIN ENGINEERING DESIGN & SELECTION 2006年第3期19卷 129-133页

作者： Madhusudhan, MS Marti-Renom, MA Sanchez, R Sali, A Univ Calif San Francisco Dept Biopharmaceut Sci San Francisco CA 94143 USA Univ Calif San Francisco Dept Pharmaceut Chem San Francisco CA 94143 USA Univ Calif San Francisco Calif Inst Quantitat Biomed Res San Francisco CA 94143 USA CUNY Mt Sinai Sch Med Struct Biol Program New York NY 10029 USA

The penalty for inserting gaps into an alignment between two protein sequences is a major determinant of the alignment accuracy. Here, we present an algorithm for finding a globally optimal alignment by dynamic programming that can use a variable gap penalty (VGP) function of any form. We also describe a specific function that depends on the structural context of an insertion or deletion. It penalizes gaps that are introduced within regions of regular secondary structure, buried regions, straight segments and also between two spatially distant residues. The parameters of the penalty function were optimized on a set of 240 sequence pairs of known structure, spanning the sequence identity range of 20-40%. We then tested the algorithm on another set of 238 sequence pairs of known structures. The use of the VGP function increases the number of correctly aligned residues from 81.0 to 84.5% in comparison with the optimized affine gap penalty function;this difference is statistically significant according to Student's t-test. We estimate that the new algorithm allows us to produce comparative models with an additional similar to 7 million accurately modeled residues in the similar to 1.1 million proteins that are detectably related to a known structure.

关键词： comparative protein structure modeling gap penalty function homology modeling sequence-structure alignment

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Comparative modeling in CASP6 using consensus approach to template selection, sequence-structure alignment, and structure assessment

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PROTEINS-structure FUNCTION AND BIOINFORMATICS 2005年第sup7期61卷 99-105页

作者： Venclovas, C Margelevicius, M Inst Biotechnol LT-02241 Vilnius Lithuania

Along with over 150 other groups we have tested our template-based protein structure prediction approach by submitting models for 30 target proteins to the sixth round of the Critical Assessment of Protein structure Prediction Methods (CASP6, http://***). Most of our modeled proteins fall into the comparative or homology modeling (CM) category, and some are fold recognition (FR) targets. The key feature of our structure prediction strategy in CASP6 was an attempt to optimally select structural templates and to make accurate sequence-structure alignments. Template selection was based mainly on consensus results of multiple sequence searches. Likewise, the consensus of multiple alignment variants (or lack of it) was used to initially delineate reliable and unreliable alignment regions. structure evaluation approaches were then used to identify the correct sequence-structure mapping. Our results suggest that in many cases use of multiple templates is advantageous. Selecting correct alignments even within the context of a three-dimensional structure remains a challenge. Together with more effective energy evaluation methods the simultaneous relaxation/refinement of a "frozen" backbone inherited from the template is likely needed to see a clear progress in tackling this problem. Our analysis also suggests that human input has little to contribute to automatic methods in modeling high homology targets. On the other hand, human expertise can be very valuable in modeling distantly related proteins and critical in cases of unexpected evolutionary changes in protein structure.

关键词： comparative modeling protein structure prediction sequence-structure alignment 3D model model evaluation distant homology alignment errors

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Learning Parameters for Non-coding RNA sequence-structure alignment

Learning Parameters for Non-coding RNA Sequence-Structure Al...

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IEEE International Conference on Bioinformatics and Biomedicine (BIBMW 2009)

作者： Song, Yinglei Liu, Chunmei Qu, Junfeng Univ MD Eastern Shore Dept Math & Comp Sci Princess Anne MD 21853 USA Howard Univ Dept Syst & Comp Sci Washington DC 20059 USA Clarion Univ Pennsylvania Dept Informat Technol Morrow GA USA

ISBN: (纸本)9781424451203

sequence-structure alignment is the most important part for an algorithm that can search genomes and identify non-coding RNAs. A model that can accurately describe the secondary structure of a noncoding RNA faamily is crucial to the search accuracy of genome annotation. In this paper we develop a novel machine learning approach that can capture the crucial structure features of a noncoding RNA family and estimate the parameters in its secondary structure Model. One advantage of this approach is that these estimated parameters contain structure features that are generally missing in the conventional Covariance Model (CM). Our experiments showed that compared with the conventional CM, structure models obtained with our approach can provide a more accurate description of the secondary structure in a noncoding RNA family and thus significantly improve the accuracy of genome annotation.

关键词： Non-coding RNA sequence-structure alignment Parameter Estimation Convex Optimization

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Predicting local quality of a sequence-structure alignment

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Journal of Bioinformatics and Computational Biology 2009年第5期7卷 789-810页

作者： Gao, Xin Xu, Jinbo Li, Shuai Cheng Li, Ming David R. Cheriton School of Computer Science University of Waterloo Waterloo ON N2L 3G1 200 University Avenue West Canada Toyota Technological Institute at Chicago Chicago IL 60637 1427 East 60th Street United States

Although protein structure prediction has made great progress in recent years, a protein model derived from automated prediction methods is subject to various errors. As methods for structure prediction develop, a continuing problem is how to evaluate the quality of a protein model, especially to identify some well-predicted regions of the model, so that the structural biology community can benefit from the automated structure prediction. It is also important to identify badly-predicted regions in a model so that some refinement measurements can be applied to it. We present two complementary techniques, FragQA and PosQA, to accurately predict local quality of a sequence-structure (i.e. sequence-template) alignment generated by comparative modeling (i.e. homology modeling and threading). FragQA and PosQA predict local quality from two different perspectives. Different from existing methods, FragQA directly predicts cRMSD between a continuously aligned fragment determined by an alignment and the corresponding fragment in the native structure, while PosQA predicts the quality of an individual aligned position. Both FragQA and PosQA use an SVM (Support Vector Machine) regression method to perform prediction using similar information extracted from a single given alignment. Experimental results demonstrate that FragQA performs well on predicting local fragment quality, and PosQA outperforms two top-notch methods, ProQres and ProQprof. Our results indicate that (1) local quality can be predicted well;(2) local sequence evolutionary information (i.e. sequence similarity) is the major factor in predicting local quality;and (3) structural information such as solvent accessibility and secondary structure helps to improve the prediction performance. © 2009 Imperial College Press.

关键词： CASP7 Local quality assessment Protein structure prediction sequence-structure alignment SVM regression

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Reconstructing the Phylogenetic Relationships of the Cyclophyllidean Cestodes: A Case Study Using ITS2 rDNA and sequence-structure alignment

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3rd International Joint Conference on Biomedical Engineering Systems and Technologies

作者： Tandon, Veena Biswal, Devendra Kumar Prasad, Pramod Kumar Malsawmtluangi, Chenkual NE Hill Univ Dept Zool Shillong 793022 Meghalaya India NE Hill Univ Bioinformat Ctr Shillong 793022 Meghalaya India

ISBN: (纸本)9783642184710

Different authors have subscribed to varied opinions on the phylogenetic relationships and systematic position of cyclophylliclean cestodes owing to high degree of non-significant morphological variations among these taxa. Molecular phylogenetic analysis based on ITS2 rDNA of 16 representatives spanning 6 different families (Mesocestoididae, Davaineidae, Anoplocephalidae, Taeniidae, Dipylidiiciae and Hymenolepididae) of the Order Cyclophyllidea and one out group from the family Diphyllobothriidae of the Order Pseudophyllidea revealed the order Order Cyclophyllidea to be a monophyletic clade. The results were further validated by bayesian analysis, primary sequence-structure alignment and subsequent molecular morphometrics analysis. A consistent support for all the major nodes was seen across all the phylogenetic trees. Interestingly, the genus Mesocestoides, in which the genital pores are ventral in position, a feature of the Order Pseudophyllidea, was accommodated within Cyclophyllidea and served as a sister clade close to the families Taeniidae, Anoplocephalidae, Hymenolepididae and Dipylidiidae.

关键词： Mesocestoides Cyclophyllidea cestodes ITS2 rDNA Molecular morphometrics sequence-structure alignment

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SYSTEMATIC POSITION AND PHYLOGENETIC RELATIONSHIPS OF THE CYCLOPHYLLIDEAN CESTODES An In-silico Study using ITS2 rDNA and sequence-structure alignment

SYSTEMATIC POSITION AND PHYLOGENETIC RELATIONSHIPS OF THE CY...

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1st International Conference on Bioinformatics (BIOINFORMATICS 2010)

作者： Tandon, Veena Biswal, Devendra Kumar Prasad, Pramod Kumar Malsawmtluangi, Chenkual North Eastern Hill Univ Dept Zool Shillong Meghalaya India North Eastern Hill Univ Bioinformat Ctr Shillong Meghalaya India

ISBN: (纸本)9789896740191

The phylogenetic relationships and systematic position of cyclophyllidean cestodes have always been controversial and opinions of different authors on the systematic rank and content of this order have varied greatly. Molecular phylogenetic analysis based on ITS2 rDNA of 16 representatives spanning 6 different families (Mesocestoididae, Davaineidae, Anoplocephalidae, Taeniidae, Dipylidiidae and Hymenolepididae) of the Order Cyclophyllidea and one out group from the family Diphyllobothriidae of the Order Pseudophyllidea confirmed the monophyletic nature of the Order Cyclophyllidea. Further, the results were validated by bayesian analysis, primary sequence-structure alignment and subsequent molecular morphometrics analysis. At the major nodes all the trees from various analyses were similar. Mesocestoides was interestingly accommodated within Cyclophyllidea and served as a sister Glade close to the families Taeniidae, Anoplocephalidae, Hymenolepididae and Dipylidiidae.

关键词： Mesocestoides Cyclophyllidea Cestodes ITS2 rDNA Molecular Morphometrics sequence-structure alignment

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sequence to structure alignment in comparative modeling using PrISM

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Proteins: structure, Function, and Bioinformatics 1999年第S3期37卷

作者： An-Suei Yang Barry Honig Columbia Genome Center and Department of Biochemistry and Molecular Biophysics Columbia University New York New York

PrISM (Protein Informatics System for Modeling) is a protein analysis and modeling system in which informatics, alignment, modeling, and assessment modules are integrated in a computational environment where protein analysis and modeling protocols can be designed and assessed interactively. It can then be used automatically and repetitively in response to a variety of protein analysis and modeling problems. PrISM was used to predict a single model for each of the 43 targets in the CASP3 experiment. In this paper, we present results for 13 target sequences, which we consider to be comparative modeling targets with clearly related structural templates. We emphasize the problem of aligning a target sequence to a template structure with various alignment methods. When more than one alignment method and/or parameter set are applied, the final alignment is chosen on the basis of a model ranking system also used in PrISM's fold recognition module. Advanced sequence–template alignment procedures in PrISM are useful in some cases when standard pairwise dynamic programming algorithm fail to make any reasonable global alignment. The same procedures, however, failed in other cases, corresponding to remotely related query-template pairs that involved extensive insertions and deletions. Proteins Suppl 1999;3:66–72. © 1999 Wiley-Liss, Inc.

关键词： protein structure modeling sequence-structure alignment PrISM: protein informatic system for modeling protein structure prediction sequence alignment error

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Position-dependent protein mutant profile based on mean force field calculation

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PROTEIN ENGINEERING 1996年第6期9卷 479-484页

作者： Wang, YL Lai, LH Li, SW Han, YZ Tang, YQ BEIJING UNIV INST PHYS CHEMBEIJING 100871PEOPLES R CHINA

The application of the mean force field in protein mutant stability prediction is explored. Based on protein main chain characteristics, including polar fraction, accessibility and dihedral angles, the mean force field was constructed to evaluate the compatibility between an amino acid residue and its environment, from which a position-dependent protein mutant profile was constructed, At each position along a protein sequence, the native residue was replaced by the other 19 types of amino acid residues, The matches were evaluated by energies from mean force field calculation, from which a mutant profile along the protein sequence was derived. General characteristics of such a profile were analyzed. Mutant stabilities for two sets of mutants in two proteins were found to be reasonable compared with experimental data, which indicates that the present method can act as a guide in protein engineering and as an effective scoring matrix in protein sequence-structure alignment studies.

关键词： inverse folding mean force field mutant profile polar fraction sequence-structure alignment

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Parameterized complexity and biopolymer sequence comparison

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COMPUTER JOURNAL 2008年第3期51卷 270-291页

作者： Cai, Liming Huang, Xiuzhen Liu, Chunmei Rosamond, Frances Song, Yinglei Univ Georgia Dept Comp Sci Athens GA 30605 USA Arkansas State Univ Dept Comp Sci State Univ AR 72467 USA Howard Univ Dept Comp Sci & Syst Washington DC 20059 USA Univ Newcastle Parameterized Complex Res Unit Auspices Off DVC Res Newcastle NSW 2308 Australia Univ Maryland Eastern Shore Dept Math & Comp Sci Prince Anne MD 21853 USA

The paper surveys parameterized algorithms and complexities for computational tasks on biopolymer sequences, including the problems of longest common subsequence, shortest common supersequence, pairwise sequence alignment, multiple sequencing alignment, structure-sequence alignment and structure-structure alignment. Algorithm techniques, built on the structural-unit level as well as on the residue level, are discussed.

关键词： parameterized complexity parameterized algorithms pairwise sequence alignment multiple sequence alignment sequence-structure alignment structure-structure alignment tree width tree decomposition RNA secondary structure recognition and protein threading

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