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Efficient construction of an assembly string graph using the FM-index

BIOINFORMATICS 2010年第12期26卷 i367-i373页

作者： Simpson, Jared T. Durbin, Richard Wellcome Trust Sanger Inst Cambridge CB10 1SA England

Motivation: Sequence assembly is a difficult problem whose importance has grown again recently as the cost of sequencing has dramatically dropped. Most new sequence assembly software has started by building a de Bruijn graph, avoiding the overlap-based methods used previously because of the computational cost and complexity of these with very large numbers of short reads. Here, we show how to use suffix array-based methods that have formed the basis of recent very fast sequence mapping algorithms to find overlaps and generate assembly string graphs asymptotically faster than previously described algorithms. Results: Standard overlap assembly methods have time complexity O(N-2), where N is the sum of the lengths of the reads. We use the Ferragina-Manzini index (FM-index) derived from the Burrows-Wheeler transform to find overlaps of length at least tau among a set of reads. As well as an approach that finds all overlaps then implements transitive reduction to produce a string graph, we show how to output directly only the irreducible overlaps, significantly shrinking memory requirements and reducing compute time to O( N), independent of depth. Overlap-based assembly methods naturally handle mixed length read sets, including capillary reads or long reads promised by the third generation sequencing technologies. the algorithms we present here pave the way for overlap-based assembly approaches to be developed that scale to whole vertebrate genome de novo assembly. Contact: js18@***

关键词： Algorithms Genomics/methods Sequence Analysis, dna/methods Software

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Real time mechanical characterization of dna in liquid during a radiotherapy treatment and its theoretical analysis

Real time mechanical characterization of dna in liquid durin...

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international conference on Solid State Sensors and Actuators (TRANSDUCERS)

作者： G. Perret T. Lacornerie F. Manca S. Giordano M. Kumemura N. Lafitte L. Jalabert E. Lartigau T. Fujii F. Cleri H. Fujita D. Collard IEMN UMR8520 CNRS University of Lille 1 France LIMMS/CNRS-IIS Japan Universite de Lille Lille Hauts-de-France FR Institute of Industrial Science The University of Tokyo Japan Tokyo Daigaku Bunkyo-ku Tokyo JP Centre Oscar Lambret University of Lille 2 France

We report the first real-time biomechanical measurement of dna bundle degradation in stable condition when exposed to a therapeutic radiation beam and a theoretical model to describe dna damages. the Silicon Nano Tweezers and their new microfluidic system endure the harsh environment of radiation beams and still retain molecular-level accuracy. this result paves the way for both fundamental and clinical studies of dna degradation under radiation for improved tumor treatment.

关键词： dna Microfluidics Degradation Cavity resonators Radiation effects Silicon Real-time systems

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Position-Defined CpG Islands Provide Complete Co-methylation Indexing for Human Genes 18th

Position-Defined CpG Islands Provide Complete Co-methylation...

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18th international conference on Intelligent computing (ICIC)

作者： Xiao, Ming Yin, Ruiying Gao, Pengbo Yu, Jun Ma, Fubo Dai, Zichun Zhang, Le Sichuan Univ Coll Comp Sci Chengdu 610065 Peoples R China Chinese Acad Sci Beijing Inst Genom CAS Key Lab Genome Sci & Informat Beijing 100101 Peoples R China Univ Chinese Acad Sci Beijing 100049 Peoples R China

ISBN: (纸本)9783031138294;9783031138287

dna methylation, especially position-sensitive co-methylation of CpG islands (CGIs), is one of the key epigenomic mechanisms of gene expression regulation and chromosomal integrity. therefore, thoroughly mapping the precise position of all CpG sequences within CGIs non-island clusters as well as their methylated status at single cell level under different physiological and pathological conditions becomes one of the ultimate goals for epigenomics. Toward this end, we compare our previously categorized position-defined CpG and methylation sites complementary to those of density-defined CpG islands to investigate patterns of such two categorized methylation sites relative to human gene expression regulation. Based on our previous analysis on LAUPs (Lineage-associated under-represented permutations) and the discovery that CpG-containing sequences are underrepresented when the distance among CpG sequences is ranged from 10bp to 14bp, we define such distances as discrete intervals at basepair precision and compute 12bp, 25bp, and 50bp, three position-defined CGIs groups according to the interval lengths, which cover 1.85 times greater CpG sites (14.98%) than those of density-defined CGIs (8.08%). this novel scheme reveals: (1) there are three partially-overlapping yet distinct position-defined CGI subgroups in the human genome. (2) the 12-bp CGIs appear unique to low-density CGIs or LCGIs but the other two CGIs, 25-bp and 50-bp, are found in all three density-defined CGIs. (3) the largest fraction of unmethylated (75.99%) and moderately-methylated (12.91%) core promoter-associated CGIs are found among the 12-bp CGIs but less found in 50-bp CGIs (41.77% for HCGIs and 20.03% for ICGI) of the same sequence region. (4) We conclude that in the Precision Medicine Era all CpG sites and their clusters are to be mapped and annotated, and modelled for gene expression regulation at single basepair precision.

关键词： Position-defined CGIs dna methylation Genome annotation High performance computing Genome analysis

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LocalMotif - An In-Silico Tool for Detecting Localized Motifs in Regulatory Sequences

LocalMotif - An In-Silico Tool for Detecting Localized Motif...

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international conference on Tools for Artificial Intelligence (ICTAI)

作者： Vipin Narang Wing-kin Sung Ankush Mittal School of Computing National University of Singapore Singapore Department of Electronics and Computer Engineering Indian Institute of Technology Roorkee Roorkee India

In silico motif finding algorithms are often used for discovering protein-dna binding sites in a set of regulatory sequences. Current algorithms mainly address motif discovery in short sequences. Analyzing long sequences can be quite challenging not only due to increasing time and memory requirements of the algorithm, but also decreasing accuracy. However, in case the motif is localized in a short interval of the long sequences relative to an anchor point, it is tenable to detect it easily by restricting the search to that interval. But the region of localization of the motif is not known a priori. this paper reports an algorithm called LocalMotif to detect localized motifs in long regulatory sequences. A novel score function predicts the region of localization of the motif. this score is combined with other scoring measures including Z-score and relative entropy to detect the motif. the algorithm is optimized for fast processing of long regulatory sequences. Tests on simulated and real datasets confirm that LocalMotif accurately determines the region of localization of motifs and automatically discovers the biologically relevant motifs, which can be detected by other motif finding algorithms only when the search is restricted to the relevant interval

关键词： Sequences dna Biological system modeling Drives Protein engineering Algorithm design and analysis Entropy Automatic testing Biology computing Genomics

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Motif Discovery as a Multiple-Instance Problem

Motif Discovery as a Multiple-Instance Problem

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international conference on Tools for Artificial Intelligence (ICTAI)

作者： Ya Zhang Yixin Chen Xiang Ji Department of EECS University of Kansas USA Department of CIS University of Mississippi USA Yahoo Inc. India

Motif discovery from bio sequences, a challenging task both experimentally and computationally, has been a topic of immense study in recent years. In this paper, we formulate the motif discovery problem as a multiple-instance problem and employ a multiple-instance learning method, the MILES method, to identify motif from biological sequences. Each sequence is mapped into a feature space defined by instances in training sequences with a novel instance-bag similarity measure. We employ I-norm SVM to select important features and construct classifiers simultaneously. these high-ranked features correspond to discovered motifs. We apply this method to discover transcriptional factor binding sites in promoters, a typical motif finding problem in biology, and show that the method is at least comparable to existing methods

关键词： Genetic mutations dna Bioinformatics Random sequences Computational Intelligence Society Biology computing Learning systems Extraterrestrial measurements Support vector machines Support vector machine classification

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Unlocking the Power of Linked Data for Metadata Enrichment 10

Unlocking the Power of Linked Data for Metadata Enrichment

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10th international conference on Computer, Control, Informatics and its Applications, IC3INA 2023

作者： Indrawati, Ariani Akbar, Zaenal Kartika, Yulia A. Saleh, Dadan R. Hayati, Anis. K. Yaman, Aris National Research and Innovation Agency Research Center for Data and Information Science Indonesia National Research and Innovation Agency Research Center for Computing Indonesia National Research and Innovation Agency Research Center for Artificial Intelligence and Cyber Security Indonesia

ISBN: (纸本)9798350394870

Effective metadata management is crucial in the era of growing digital repositories and abundant information. Traditional metadata may not provide sufficient depth and richness for comprehensive insights in many repositories. Metadata enrichment techniques are increasingly used to address this issue by adding valuable information from other resources. Two metadata enrichment methods are examined: using Wikidata as a central hub and directly querying relevant repositories. We present a case study on the Indonesia Nucleotide Archive (InNA), a dna/RNA data repository, to evaluate the effectiveness of these methods. Our findings showed that both enrichment methods have advantages and considerations. We discovered that 18 out of the total 27 species exhibited potential for enrichment, although with varying levels of comprehensiveness, by utilizing Wikidata as a central resource. On the other hand, directly querying pertinent repositories resulted in a significantly greater quantity of valuable information for each of the 27 species. the enrichment result suggests that the process of enhancing metadata has a substantial impact on enhancing the contextualization of resources within the InNA. this includes various attributes such as taxonomy, morphology, culture, ecological data, molecular biology, relevant links, etc. © 2023 IEEE.

关键词： Metadata

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DOUBLE-STRAND BREAKS FROM I-125 INCORPORATED IN thE dna AND CELL-DEAth

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international JOURNAL OF RADIATION BIOLOGY 1994年第5期66卷 437-440页

作者： CHARLTON, DE HOFER, KG VANLOON, N SCHNEIDERMAN, MH FLORIDA STATE UNIV TALLAHASSEEFL 32306 UNIV CALIF SAN FRANCISCO SAN FRANCISCOCA 94143 UNIV NEBRASKA MED CTRLINCOLNNE 68583

Track structure calculations of the local energy deposition by electrons emitted during the decay of I-125 are used to demonstrate that the range of high energy deposition is small (< 10 nm) and restricted to the dna and its immediate environment. An experiment in which I-125 is incorporated into the dna of synchronized CHO cells during a pulse and decays are allowed to accumulate a given time after the incorporation is described. Here it is shown that damage from I-125 decays in newly replicated dna (cells frozen for decay accumulation within Ih after labelling) are relatively non-toxic whereas decays in mature dna (cells frozen 5h after labelling) are highly lethal. It is suggested that during dna maturation the labelled dna becomes associated with (or reorganized into) a radiosensitive nuclear structure and that damage to this structure is the primary cause of radiation-induced cell death.

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[Regular Paper] A High-Performance Sequence Analysis Engine for Shotgun Metagenomics through GPU Acceleration

[Regular Paper] A High-Performance Sequence Analysis Engine ...

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IEEE Symposium on Bioinformatics and Bioengineering (BIBE)

作者： Ying-Feng Hsu Morito Matsuoka Nicolas Jung Yuki Matsumoto Daisuke Motooka Shota Nakamura Cybermedia Center Osaka University Osaka Japan Genome Information Research Center Osaka University Osaka Japan

ISBN: (纸本)9781538650431;9781538662175

With the continual growth of low-cost and high-throughput dna sequence technology, the scale and amount of next-generation sequencing (NGS) datasets are continually increasing in many genomics research areas. Shotgun metagenomics sequencing provides comprehensive information on microorganisms, based on complex samples of the ecosystem. Due to challenges of its scale and computational complexity, efficient sequence processing and analyzing tools are needed. In this paper, we propose a novel high-performance shotgun metagenomics sequence analysis engine for the task of sequence comparison. It includes two major components. First, a customized shifting database, which is optimized from any existing dna sequence dataset. Second, a high-performance sequence computation algorithm that utilizes the customized shifting reference database and accelerates GPU parallel computing. We elaborated upon the efficiency and computational complexity of our proposed approach in an HPC server, which has eight Nvidia Tesla P100 GPUs. We also conducted a case study to detect viral sequences from patients' blood samples. Our experimental result shows that we obtain similar accuracy to the conventional BLAST method, but with a computational speed that is about twenty times faster.

关键词： Graphics processing units dna Databases Sequential analysis Engines Bioinformatics Acceleration

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Comparison of PCR assays with direct microscopy for diagnosis of cutaneous leishmaniasis patients reported from Sindh, Pakistan

Comparison of PCR assays with direct microscopy for diagnosi...

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international Bhurban conference on Applied Sciences & Technology, IBCAST

作者： Irfan Ali Jameela Akhtar Erum Shoeb Nuzhat Ahmed CESAT Islamabad Center for Molecular Genetics (CMG) University of Karachi Pakistan

the objectives of this study was the molecular identification of Leishmania species and evaluate the diagnostic yield of PCR in comparison to the direct microscopy. this study was conducted at Centre for molecular Genetics, University of Karachi, from March 2007 - December 2011. Samples were taken by means of Saline Aspirate (SA) from 50 patients suspected of cutaneous leishmaniasis (CL) from Dermatology Department, Jinnah Post Graduate Medical College, Karachi, Pakistan from March 2007 - December 2008. Only four samples (8%) had microscopically positive results. Recovery of parasites in cultures was of 09 strains (18%). these strains were maintained in vitro for the purpose of diagnosis by PCR and vaccine preparation. three strains were vanished due to bacterial contamination. the remaining 06 culture positive samples along with saline aspirate obtained from all 50 patients. Sore were confirmed for the presence of Leishmania species by PCR method. Electrophoresis pattern from each isolates were compared with reference strains for L. major (MRHO/IR/75/ER), L. tropica (MHOM/SU/74/K27) and L. infantum (MHOM/TN/80/IPTI). Hundred percent isolates subjected to PCR, were similar to L. major (MRHO/IR/75/ER) reference strain. All of these PCR products showed a single band of approximately 650bp representing Leishmania major specific Kinetoplast dna (kdna) sequences. this 650bp band was of same size as that of the standard identified Leishmania strain. In conclusion CL caused by L. major infection is prevalent in the Sindh province of Pakistan. this study also proves that PCR method is sensitive diagnostic test in comparison to the direct microscopy.

关键词： dna Strain Microscopy Educational institutions Polymers Purification

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Prevalence and diagnosis of Hepatitis B virus based on Polymerase Chain Reaction (PCR) in district Noshki Balochistan

Prevalence and diagnosis of Hepatitis B virus based on Polym...

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international Bhurban conference on Applied Sciences & Technology, IBCAST

作者： Sanaullah Badeni Alam Mengal Hajirah Dotani Zia ul Haq Fawad Ali Hameed Baloch Mohammad Assif BUETIMS Quetta Pakistan CASVAB Quetta Pakistan Charage Diagnostic Centre (CDC) Lab Lahore Pakistan Live-Stock Department Quetta Pakistan

Hepatitis B virus (HBV) is major causative agent of chronic liver disease that leads to cirrhosis or hepatocellular carcinoma (HCC). It is estimated that about 5% patients became chronic carriers of this pathogen in Pakistan. HBV diagnosis is the most important for the patient treatment and vaccination. Serological tests are used to distinguish acute, self limited infections from chronic HBV infections and to monitor vaccine induced immunity. Nucleic acid testing for HBV-dna by PCR is increasingly being used to quantify HBV viral load and measure the effectiveness of therapeutic agents. the aim of this study is to determine the prevalence of HBV in Noshki, Baluchistan. the study was conducted from September to December 2013 in Baluchistan University of Engineering Technology Information Management Sciences (BUETIMS) Quetta, Baluchistan. One hundred immunochromatography test (ICT) positive samples were collected for the analysis of HBV using nested PCR. Out of 100 subjects (64%) subjects were male and (36%) subjects were female having four different age groups between 15-60 years. A total of (4.0%) subjects were found positive for HBV dna. Age, gender, literacy and marital status were determined. the prevalence of HBV infection was found more in age group 4 (51-60 years) than age group 1(15-30) and 3(41-50). there was no HBV dna found in age group 2. the high prevalence HBV percentage was observed for males (4.78%) than females (2.69%). However, significantly increased association was found in illiterate population (6.0%) than literate population (2.0%). Higher prevalence rate of HBV was observed in married subjects (4.69%) than unmarried 2.78%). In conclusion the molecular diagnosis of HBV by Nested-PCR is more sensitive and specific for the determination HBV dna. the prevalence and incidence of HBV in present study is alarming. the control and prevention of the local population from this fatal liver disease needs immediate attention.

关键词： dna Blood Sociology Statistics Hospitals Polymers Liver diseases

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