Pub Date : 2007-12-01DOI: 10.1142/9781848161092_0036
B. Dasgupta, Jin-Hunh Jun, I. Măndoiu
Primer Approximation Multiplex PCR (PAMP) is a recently introduced experimental technique for detecting large-scale cancer genome lesions such as inversions and deletions from heterogeneous samples containing a mixture of cancer and normal cells. In this paper we give integer linear programming formulations for the problem of selecting sets of PAMP primers that minimize detection failure probability. We also show that PAMP primer selection for detection of anchored deletions cannot be approximated within a factor of 2 ", and give a 2-approximation algorithm for a special case of the problem. Experimental results show that our ILP formulations can be used to optimally solve medium size instances of the inversion detection problem, and that heuristics based on iteratively solving ILP formulations for a one-sided version of the problem give near-optimal solutions for anchored deletion detection with highly scalable runtime.
{"title":"Primer Selection Methods for Detection of Genomic Inversions and Deletions via PAMP","authors":"B. Dasgupta, Jin-Hunh Jun, I. Măndoiu","doi":"10.1142/9781848161092_0036","DOIUrl":"https://doi.org/10.1142/9781848161092_0036","url":null,"abstract":"Primer Approximation Multiplex PCR (PAMP) is a recently introduced experimental technique for detecting large-scale cancer genome lesions such as inversions and deletions from heterogeneous samples containing a mixture of cancer and normal cells. In this paper we give integer linear programming formulations for the problem of selecting sets of PAMP primers that minimize detection failure probability. We also show that PAMP primer selection for detection of anchored deletions cannot be approximated within a factor of 2 \", and give a 2-approximation algorithm for a special case of the problem. Experimental results show that our ILP formulations can be used to optimally solve medium size instances of the inversion detection problem, and that heuristics based on iteratively solving ILP formulations for a one-sided version of the problem give near-optimal solutions for anchored deletion detection with highly scalable runtime.","PeriodicalId":74513,"journal":{"name":"Proceedings of the ... Asia-Pacific bioinformatics conference","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2007-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85861917","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2007-12-01DOI: 10.1142/9781848161092_0013
Ryuichiro Nakato, O. Gotoh
National Institute of Advanced Industrial Science and Technology,Computational Biology Research Center,2-42 Aomi, Koto-ku, Tokyo 135-0064, JapanGenomic sequence alignment is a powerful tool for finding com mon subsequence patterns sharedby the input sequences and identifying evolutionary relationships between the species. However, therunning time and space requirement of genome alignment have often been very extensive. In thisresearch, we propose a novel algorithm called Coarse-Grained AlignmenT (CGAT) algorithm, forreducing computational complexity necessary for cross-species whole genome sequence alignment.The CGAT first divides the input sequences into ”blocks” with a fixed length and aligns these blocksto each other. The generated block-level alignment is then refined at the nucleotide level. This two-stepprocedure can drastically reduce the overall computational time and space necessary for an alignment.In this paper, we show the effectiveness of the proposed algorithm by applying it to whole genomesequences of several bacteria.Keywords: Genome Alignment; Multiple Alignment; Sequence Analysis; Comparative Genomics.
{"title":"A Novel Method for Reducing Computational Complexity of Whole Genome Sequence Alignment","authors":"Ryuichiro Nakato, O. Gotoh","doi":"10.1142/9781848161092_0013","DOIUrl":"https://doi.org/10.1142/9781848161092_0013","url":null,"abstract":"National Institute of Advanced Industrial Science and Technology,Computational Biology Research Center,2-42 Aomi, Koto-ku, Tokyo 135-0064, JapanGenomic sequence alignment is a powerful tool for finding com mon subsequence patterns sharedby the input sequences and identifying evolutionary relationships between the species. However, therunning time and space requirement of genome alignment have often been very extensive. In thisresearch, we propose a novel algorithm called Coarse-Grained AlignmenT (CGAT) algorithm, forreducing computational complexity necessary for cross-species whole genome sequence alignment.The CGAT first divides the input sequences into ”blocks” with a fixed length and aligns these blocksto each other. The generated block-level alignment is then refined at the nucleotide level. This two-stepprocedure can drastically reduce the overall computational time and space necessary for an alignment.In this paper, we show the effectiveness of the proposed algorithm by applying it to whole genomesequences of several bacteria.Keywords: Genome Alignment; Multiple Alignment; Sequence Analysis; Comparative Genomics.","PeriodicalId":74513,"journal":{"name":"Proceedings of the ... Asia-Pacific bioinformatics conference","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2007-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79240518","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2007-12-01DOI: 10.1142/9781848161092_0039
Juntao Li, M. Eshaghi, Jianhua Liu, K. R. K. Murthy
DNA replication is a key process in cell division cycle. It is initiated in coordinated manner in several species. To understand the DNA replication in a species one needs to measure the half replication timing (or replication timing) and the efficiency of replication which vary across genome in higher eukaryotes. In the previous studies, no direct assessment of replication efficiency on a genomic scale was performed while the replication timing was indirectly assessed using average DNA. In this paper, we present a first-ever-method of directly measuring both half replication timing and efficiency simultaneously from a single DNA microarray time-course data. We achieve it by fitting the so called near-sigmoid model to each locus of the DNA. We use this model apply S. pombe DNA replication microarray data and show that it is effective for genome-scale replication timing and efficiency profiling studies.
{"title":"Near-sigmoid Modeling to Simultaneously Profile Genome-wide DNA Replication Timing and Efficiency in Single DNA Replication Microarray Studies","authors":"Juntao Li, M. Eshaghi, Jianhua Liu, K. R. K. Murthy","doi":"10.1142/9781848161092_0039","DOIUrl":"https://doi.org/10.1142/9781848161092_0039","url":null,"abstract":"DNA replication is a key process in cell division cycle. It is initiated in coordinated manner in several species. To understand the DNA replication in a species one needs to measure the half replication timing (or replication timing) and the efficiency of replication which vary across genome in higher eukaryotes. In the previous studies, no direct assessment of replication efficiency on a genomic scale was performed while the replication timing was indirectly assessed using average DNA. In this paper, we present a first-ever-method of directly measuring both half replication timing and efficiency simultaneously from a single DNA microarray time-course data. We achieve it by fitting the so called near-sigmoid model to each locus of the DNA. We use this model apply S. pombe DNA replication microarray data and show that it is effective for genome-scale replication timing and efficiency profiling studies.","PeriodicalId":74513,"journal":{"name":"Proceedings of the ... Asia-Pacific bioinformatics conference","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2007-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87765619","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2007-12-01DOI: 10.1142/9781848161092_0012
Thomas K. F. Wong, Y. Chiu, T. Lam, S. Yiu
In this paper, we consider the problem of structural alignment of a target RNA sequence of length n and a query RNA sequence of length m with known secondary structure that may contain embedded simple pseduoknots. The best known algorithm for solving this problem (Dost et al. [13]) runs in O(mn4) time with space complexity of O(mn3), which requires too much memory making it infeasible for comparing ncRNAs (non-coding RNAs) with length several hundreds or more. We propose a memory efficient algorithm to solve the same problem. We reduce the space complexity to O(mn2 + n3) while maintaining the same time complexity of Dost et al.’s algorithm. Experimental reslts show that our algorithm is feasible for comparing ncRNAs of length more than 500. Availability: The source code of our program is available upon request.
{"title":"A Memory Efficient Algorithm for Structural Alignment of RNAs with Embedded Simple Pseudoknots","authors":"Thomas K. F. Wong, Y. Chiu, T. Lam, S. Yiu","doi":"10.1142/9781848161092_0012","DOIUrl":"https://doi.org/10.1142/9781848161092_0012","url":null,"abstract":"In this paper, we consider the problem of structural alignment of a target RNA sequence of length n and a query RNA sequence of length m with known secondary structure that may contain embedded simple pseduoknots. The best known algorithm for solving this problem (Dost et al. [13]) runs in O(mn4) time with space complexity of O(mn3), which requires too much memory making it infeasible for comparing ncRNAs (non-coding RNAs) with length several hundreds or more. We propose a memory efficient algorithm to solve the same problem. We reduce the space complexity to O(mn2 + n3) while maintaining the same time complexity of Dost et al.’s algorithm. Experimental reslts show that our algorithm is feasible for comparing ncRNAs of length more than 500. Availability: The source code of our program is available upon request.","PeriodicalId":74513,"journal":{"name":"Proceedings of the ... Asia-Pacific bioinformatics conference","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2007-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76985733","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2007-12-01DOI: 10.1142/9781848161092_0028
M. Abouelhoda, R. Giegerich, B. Behzadi, J. Steyaert
In addition to the well-known edit operations, the alignment of minisatellite maps includes duplication events. We model these duplications using a special kind of spanning trees and deduce an optimal duplication scenario by computing the respective minimum spanning tree. Based on best duplication scenarios for all substrings of the given sequences, we compute an optimal alignment of two minisatellite maps. Our algorithm improves upon the previously developed algorithms in the generality of the model, in alignment quality and in space-time efficiency. Using this algorithm, we derive evidence that there is a directional bias in the growth of minisatellites of the MSY1 dataset.
{"title":"Alignment of Minisatellite Maps: A Minimum Spanning Tree-based Approach","authors":"M. Abouelhoda, R. Giegerich, B. Behzadi, J. Steyaert","doi":"10.1142/9781848161092_0028","DOIUrl":"https://doi.org/10.1142/9781848161092_0028","url":null,"abstract":"In addition to the well-known edit operations, the alignment of minisatellite maps includes duplication events. We model these duplications using a special kind of spanning trees and deduce an optimal duplication scenario by computing the respective minimum spanning tree. Based on best duplication scenarios for all substrings of the given sequences, we compute an optimal alignment of two minisatellite maps. Our algorithm improves upon the previously developed algorithms in the generality of the model, in alignment quality and in space-time efficiency. Using this algorithm, we derive evidence that there is a directional bias in the growth of minisatellites of the MSY1 dataset.","PeriodicalId":74513,"journal":{"name":"Proceedings of the ... Asia-Pacific bioinformatics conference","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2007-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83841317","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2007-12-01DOI: 10.1142/9781848161092_0019
Jin-Dong Kim, Tomoko Ohta, Kanae Oda, Junichi Tsujii
We present a new direction of research, which deploys Text Mining technologies to construct and maintain data bases organized in the form of pathway, by associating parts of papers with relevant portions of a pathway and vice versa. In order to materialize this scenario, we present two annotated corpora. The first, Event Annotation, identifies the spans of text in which biological events are reported, while the other, Pathway Annotation, associates portions of papers with specific parts in a pathway.
{"title":"From Text to Pathway: Corpus Annotation for Knowledge Acquisition from Biomedical Literature","authors":"Jin-Dong Kim, Tomoko Ohta, Kanae Oda, Junichi Tsujii","doi":"10.1142/9781848161092_0019","DOIUrl":"https://doi.org/10.1142/9781848161092_0019","url":null,"abstract":"We present a new direction of research, which deploys Text Mining technologies to construct and maintain data bases organized in the form of pathway, by associating parts of papers with relevant portions of a pathway and vice versa. In order to materialize this scenario, we present two annotated corpora. The first, Event Annotation, identifies the spans of text in which biological events are reported, while the other, Pathway Annotation, associates portions of papers with specific parts in a pathway.","PeriodicalId":74513,"journal":{"name":"Proceedings of the ... Asia-Pacific bioinformatics conference","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2007-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80663458","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2007-12-01DOI: 10.1142/9781848161092_0033
D. Konovalov, D. Heg
Estimations of population genetic parameters like allele frequencies, heterozygosities, inbreeding coefficients and genetic distances rely on the assumption that all sampled genotypes come from a randomly interbreeding population or sub-population. Here we show that small cross-generational samples may severely affect estimates of allele frequencies, when a small number of progenies dominate the next generation or the sample. A new estimator of allele frequencies is developed for such cases when the kin structure of the focal sample is unknown and has to be assessed simultaneously. Using Monte Carlo simulations it was demonstrated that the new estimator delivered significant improvement over the conventional allele counting estimator.
{"title":"Estimation of Population Allele Frequencies from Small Samples Containing Multiple Generations","authors":"D. Konovalov, D. Heg","doi":"10.1142/9781848161092_0033","DOIUrl":"https://doi.org/10.1142/9781848161092_0033","url":null,"abstract":"Estimations of population genetic parameters like allele frequencies, heterozygosities, inbreeding coefficients and genetic distances rely on the assumption that all sampled genotypes come from a randomly interbreeding population or sub-population. Here we show that small cross-generational samples may severely affect estimates of allele frequencies, when a small number of progenies dominate the next generation or the sample. A new estimator of allele frequencies is developed for such cases when the kin structure of the focal sample is unknown and has to be assessed simultaneously. Using Monte Carlo simulations it was demonstrated that the new estimator delivered significant improvement over the conventional allele counting estimator.","PeriodicalId":74513,"journal":{"name":"Proceedings of the ... Asia-Pacific bioinformatics conference","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2007-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84068953","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2007-12-01DOI: 10.1142/9781848161092_0011
Oliver Sander, F. S. Domingues, Hongbo Zhu, Thomas Lengauer, Ingolf Sommer
Structural bioinformatics provides new tools for investigating protein-protein interactions at the molecular level. We present two types of structural descriptors for efficiently representing and comparing protein-protein binding sites and surface patches. The descriptors are based on distributions of distances between five types of functional atoms, thereby capturing the spatial arrangement of physicochemical properties in 3D space. Experiments with the method are performed on two tasks: (1) detection of binding sites with known similarity from homologous proteins, and (2) scanning of the surfaces of two non-homologous proteins for similar regions.
{"title":"Structural Descriptors of Protein-Protein Binding Sites","authors":"Oliver Sander, F. S. Domingues, Hongbo Zhu, Thomas Lengauer, Ingolf Sommer","doi":"10.1142/9781848161092_0011","DOIUrl":"https://doi.org/10.1142/9781848161092_0011","url":null,"abstract":"Structural bioinformatics provides new tools for investigating protein-protein interactions at the molecular level. We present two types of structural descriptors for efficiently representing and comparing protein-protein binding sites and surface patches. The descriptors are based on distributions of distances between five types of functional atoms, thereby capturing the spatial arrangement of physicochemical properties in 3D space. Experiments with the method are performed on two tasks: (1) detection of binding sites with known similarity from homologous proteins, and (2) scanning of the surfaces of two non-homologous proteins for similar regions.","PeriodicalId":74513,"journal":{"name":"Proceedings of the ... Asia-Pacific bioinformatics conference","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2007-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74807030","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2007-12-01DOI: 10.1142/9781848161092_0003
A. Valencia
A compact and low profile document handling unit with short and simple document recirculation paths for recirculating a set of original document sheets to and from one side of the platen of a copier with or without inversion for selective repeated copying of one or both sides of the documents, in which the selectable document inverter in the document recirculation path includes a generally planar document sheet reversing chute which is generally parallel to and closely overlying the platen and a sheet reversing feeder adjacent the same side of the platen for feeding the document sheets into the reversing chute directly from the platen, but inverted, and for feeding them out of the reversing chute to a restacking tray at that same side of the platen without inversion.
{"title":"Protein Interactions Extracted from Genomes and Papers","authors":"A. Valencia","doi":"10.1142/9781848161092_0003","DOIUrl":"https://doi.org/10.1142/9781848161092_0003","url":null,"abstract":"A compact and low profile document handling unit with short and simple document recirculation paths for recirculating a set of original document sheets to and from one side of the platen of a copier with or without inversion for selective repeated copying of one or both sides of the documents, in which the selectable document inverter in the document recirculation path includes a generally planar document sheet reversing chute which is generally parallel to and closely overlying the platen and a sheet reversing feeder adjacent the same side of the platen for feeding the document sheets into the reversing chute directly from the platen, but inverted, and for feeding them out of the reversing chute to a restacking tray at that same side of the platen without inversion.","PeriodicalId":74513,"journal":{"name":"Proceedings of the ... Asia-Pacific bioinformatics conference","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2007-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79945046","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2007-12-01DOI: 10.1142/9781848161092_0004
Wen-Yun Yang, Bao-Liang Lu
We introduce a general framework for string kernels. This framework can produce various types of kernels, including a number of existing kernels, to be used with support vector machines (SVMs). In this framework, we can select the informative subsequences to reduce the dimensionality of the feature space. We can model the mutations in biological sequences. Finally, we combine contributions of subsequences in a weighted fashion to get the target kernel. In practical computation, we develop a novel tree structure, coupled with a traversal algorithm to speed up the computation. The experimental results on a benchmark SCOP data set show that the kernels produced by our framework outperform the existing spectrum kernels, in both e‐ciency and ROC50 scores.
{"title":"String Kernels with Feature Selection for SVM Protein Classification","authors":"Wen-Yun Yang, Bao-Liang Lu","doi":"10.1142/9781848161092_0004","DOIUrl":"https://doi.org/10.1142/9781848161092_0004","url":null,"abstract":"We introduce a general framework for string kernels. This framework can produce various types of kernels, including a number of existing kernels, to be used with support vector machines (SVMs). In this framework, we can select the informative subsequences to reduce the dimensionality of the feature space. We can model the mutations in biological sequences. Finally, we combine contributions of subsequences in a weighted fashion to get the target kernel. In practical computation, we develop a novel tree structure, coupled with a traversal algorithm to speed up the computation. The experimental results on a benchmark SCOP data set show that the kernels produced by our framework outperform the existing spectrum kernels, in both e‐ciency and ROC50 scores.","PeriodicalId":74513,"journal":{"name":"Proceedings of the ... Asia-Pacific bioinformatics conference","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2007-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78179524","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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