2009 Ohio Collaborative Conference on Bioinformatics最新文献

A New Method for Mapping Short DNA Sequencing Reads by Using Quality Scores 一种利用质量分数定位DNA短序列的新方法

2009 Ohio Collaborative Conference on Bioinformatics Pub Date : 2009-06-15 DOI: 10.1109/OCCBIO.2009.35

H. Ozer, Terry Camerlengo, T. Huang, Kun Huang

{"title":"A New Method for Mapping Short DNA Sequencing Reads by Using Quality Scores","authors":"H. Ozer, Terry Camerlengo, T. Huang, Kun Huang","doi":"10.1109/OCCBIO.2009.35","DOIUrl":"https://doi.org/10.1109/OCCBIO.2009.35","url":null,"abstract":"New high-throughput sequencing technologies can generate millions of short DNA sequences that need to be mapped to the reference genome accurately. Majority of the mapping algorithms handle variations in the quality of these short sequences by allowing more mismatches and/or gaps in the alignment and focus to improve runtime. In this paper, weinvestigate ways to classify quality scores of short DNA sequencing reads and integrate them into the mapping process. We specifically studied the quality scores that suggest two alternate bases (the top quality scores for two bases are close to each other at the locus) and use of such bases to improve mapping accuracy.Our method includes generation of alternative sequences when there are alternate-quality bases in a sequence read and mapping of these alternative sequences to the reference genome. In a test using a piece of ChIP-seq data from epigenetic study, we generated and mapped alternatives of 222,755 sequence reads (out of the original 2.5 million reads) that cannot be mapped to the reference genome by the Eland algorithm. With this approach we could be able to map 12.8% of these sequence reads with alternative bases to unique positions in the genome. In this study, we demonstrate that use of alternative bases in mapping algorithms can improve mapping results dramatically.","PeriodicalId":231499,"journal":{"name":"2009 Ohio Collaborative Conference on Bioinformatics","volume":"718 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2009-06-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"116764361","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}

引用次数: 1

HIV Evolution: Fast or Slow? HIV进化:快还是慢?

2009 Ohio Collaborative Conference on Bioinformatics Pub Date : 2009-06-15 DOI: 10.1109/OCCBIO.2009.34

H. Piontkivska, S. Paul

引用次数: 0

Comparative Assessment of DNA Assemblers for Assembling Expressed Sequence Tags 表达序列标签的DNA组装器的比较评估

2009 Ohio Collaborative Conference on Bioinformatics Pub Date : 2009-06-15 DOI: 10.1109/OCCBIO.2009.19

X. Min, G. Butler, R. Storms, A. Tsang

{"title":"Comparative Assessment of DNA Assemblers for Assembling Expressed Sequence Tags","authors":"X. Min, G. Butler, R. Storms, A. Tsang","doi":"10.1109/OCCBIO.2009.19","DOIUrl":"https://doi.org/10.1109/OCCBIO.2009.19","url":null,"abstract":"Assembling expressed sequence tags (ESTs) is essential for removing redundancy and generating long virtual transcripts for EST annotation and gene finding. A number of assemblers are available, but there is a lack of detailed comparative assessment of the strength and weakness of these assemblers. We compared three assemblers including Phrap, CAP3 and TIGR Assembler (TA) using Aspergillus niger and Phanerochaete chrysosporium EST data. Phrap assembled more ESTs into contigs than TA and CAP3. Among the contigs and singletons generated by the three assemblers, 67 – 90% of them were identical. The number of contigs and singletons assembled by Phrap provides an estimate of the maximum number of unique genes represented in the dataset, while the numbers generated by TA and CAP3 provide an approximate estimate of unique transcripts since both TA and CAP are more discriminating to alternatively spliced transcripts. The error rate in contigs generated by Phrap was slightly higher than contigs generated by TA or CAP3. Phrap is thus recommended for EST assembling aiming at generating a set of unisequences with minimum redundancy for estimating the unigene number, and TA or CAP3 are used for assembling ESTs aiming at finding unique transcripts, i. e., for identification of alternative splicing.","PeriodicalId":231499,"journal":{"name":"2009 Ohio Collaborative Conference on Bioinformatics","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2009-06-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128576619","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}

引用次数: 3

Comparison of Label Free and 18 O Labeling Mass Spectrometry in Relative Protein Quantification 无标记质谱法和18o标记质谱法在相对蛋白质定量中的比较

2009 Ohio Collaborative Conference on Bioinformatics Pub Date : 2009-06-15 DOI: 10.1109/OCCBIO.2009.28

Chao Yuan, Gaurav S. J. B. Rana, Jinsook Chang, R. Ewing, M. Chance

引用次数: 0

Perceived Cost of Auxotrophic Amino Acids in Two Bacterial Species 两种细菌中营养不良氨基酸的感知成本

2009 Ohio Collaborative Conference on Bioinformatics Pub Date : 2009-06-15 DOI: 10.1109/OCCBIO.2009.22

Esley Heizer, Douglas W. Raiford, M. Raymer, D. Krane

{"title":"Perceived Cost of Auxotrophic Amino Acids in Two Bacterial Species","authors":"Esley Heizer, Douglas W. Raiford, M. Raymer, D. Krane","doi":"10.1109/OCCBIO.2009.22","DOIUrl":"https://doi.org/10.1109/OCCBIO.2009.22","url":null,"abstract":"Amino acid biosynthetic pathways are highly conserved throughout all domains of life. Biosynthesis of amino acid requires the diversion of resources from energy production to amino acid production. The consequent energy-cost of producing an individual amino acid is can be estimated by addingthe amount of ATP expended in production itself to the amount of potential energy lost. Some organisms lack the metabolic pathways required for the synthesis of some or all of their amino acids and must obtain them from their environment or their host organism. The energetic costs associated with this means of obtaining amino acids are largely a matter of speculation at the present time. This study examines the perceived cost of auxotrophic amino acids (amino acids an organism is unable to synthesize) in two bacteria (Bacillus cereus ATCC 10987 andVibrio fischeri ES114). Auxotrophic amino acids in bothorganisms were found to be used preferentially in highlyexpressed genes and are therefore likely to be energetically inexpensive relative to those the organisms are capable of synthesizing themselves. A regression approach was used tocomputationally estimate the perceived costs to the organism.","PeriodicalId":231499,"journal":{"name":"2009 Ohio Collaborative Conference on Bioinformatics","volume":"14 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2009-06-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134166793","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}

引用次数: 1

RNA Secondary Structure Prediction in the Presence of Single-Stranded Binding Proteins 单链结合蛋白存在下的RNA二级结构预测

2009 Ohio Collaborative Conference on Bioinformatics Pub Date : 2009-06-15 DOI: 10.1109/OCCBIO.2009.17

Robert A. Forties, R. Bundschuh

引用次数: 0

Discovery of Regulatory Networks in Plants by Linking Promoter and Transcription Factor Databases 通过连接启动子和转录因子数据库发现植物调控网络

2009 Ohio Collaborative Conference on Bioinformatics Pub Date : 2009-06-15 DOI: 10.1109/OCCBIO.2009.13

A. Yilmaz, R. Davuluri, Saranyan K. Palaniswamy, E. Grotewold

{"title":"Discovery of Regulatory Networks in Plants by Linking Promoter and Transcription Factor Databases","authors":"A. Yilmaz, R. Davuluri, Saranyan K. Palaniswamy, E. Grotewold","doi":"10.1109/OCCBIO.2009.13","DOIUrl":"https://doi.org/10.1109/OCCBIO.2009.13","url":null,"abstract":"Transcription factors (TFs) control the levels as well as the sites and times of expression of a discrete set of target genes by binding to specific cis-regulatory elements in the corresponding promoter regions. They can function as master control switches for the regulation of metabolic pathways, cell differentiation and the cell cycle. Thus, the state of a living cell is the result of regulated transcription of thousands of genes in which TFs are major players. A first step in the discovering the regulatory networks is to establish the organization of cis-elements in promoters and the direct targets of TFs. Towards this goal, our lab has developed two publicly available TF and promoter databases. AGRIS (arabidopsis.med.ohio-state.edu) is dedicated to reveal regulatory networks in Arabidopsis and is currently composed of databases of putative cis-elements (AtcisDB) and TFs (AtTFDB). The regulatory network in Arabidopsis is constructed based on available data by linking cis-regulatory elements and transcription factors, interactions that are visualized by AtRegNet.GRASSIUS (grassius.org) provides regulatory information gathered from computational and experimental sources for the grasses, initially including maize, rice, sorghum and sugarcane. Promoter sequences across these grasses and cis-elements important for gene expression are gathered in GrassPROMDB. GrassTFDB contains information on TFs, their DNA-binding properties and the genes that they have been experimentally demonstrated to bind/regulate. GrassREGNET is the ultimate component of GRASSIUS, currently under development, and will provide a dynamic relationship between the contents of GrassTFDB and GrassPROMDB in the light of experimentally verified interactions, helping visualize spatio-temporal gene regulation and regulatory networks.","PeriodicalId":231499,"journal":{"name":"2009 Ohio Collaborative Conference on Bioinformatics","volume":"6 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2009-06-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132916526","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}

引用次数: 0

Parallel Approaches for SWAMP Sequence Alignment SWAMP序列比对的并行方法

2009 Ohio Collaborative Conference on Bioinformatics Pub Date : 2009-06-15 DOI: 10.1109/OCCBIO.2009.12

Shannon Steinfadt, K. Schaffer

引用次数: 2

Construction of Genomic Regulatory Encyclopedias: Strategies and Case Studies 基因组调控百科全书的构建:策略与案例研究

2009 Ohio Collaborative Conference on Bioinformatics Pub Date : 2009-06-15 DOI: 10.1109/OCCBIO.2009.9

J. Lichtenberg, Mohit Alam, Thomas Bitterman, Frank Drews, Klaus H. Ecker, L. Elnitski, S. Evans, Matt Geisler, E. Grotewold, Dazhang Gu, E. Jacox, K. Kurz, Stephen Lee, Xiaoyu Liang, P. Majmudar, Paul Morris, Chase W. Nelson, E. Stockinger, Joshua D. Welch, S. Wyatt, Alper Yilmaz, L. Welch

引用次数: 0

xIP-seq Platform: An Integrative Framework for High-Throughput Sequencing Data Analysis xIP-seq平台:高通量测序数据分析的综合框架

2009 Ohio Collaborative Conference on Bioinformatics Pub Date : 2009-06-15 DOI: 10.1109/OCCBIO.2009.20

Xin Wang, Mingxiang Teng, Guohua Wang, Yuming Zhao, Xu Han, Weixing Feng, Lang Li, J. Sanford, Yunlong Liu

{"title":"xIP-seq Platform: An Integrative Framework for High-Throughput Sequencing Data Analysis","authors":"Xin Wang, Mingxiang Teng, Guohua Wang, Yuming Zhao, Xu Han, Weixing Feng, Lang Li, J. Sanford, Yunlong Liu","doi":"10.1109/OCCBIO.2009.20","DOIUrl":"https://doi.org/10.1109/OCCBIO.2009.20","url":null,"abstract":"We report an integrative bioinformatic platform for next-generation sequencing data analysis, xIP-seq, which is built on GenePattern package. The purpose for this tool is to provide analysis pipelines for data derived from next-generation sequencing following a variety of experiments using immunoprecipitation, such as ChIP-seq (chromatin immunoprecipitation following sequencing) for analysis of DNA binding protein, CLIP-seq (cross-linking immunoprecipitation following sequencing) for analysis of RNA binding protein, and MeDIP-seq (methylation DNA immunoprecipitation following sequencing) for DNA methylation profiles. xIP-seq platform provides standardized data pre-processing workflows which prepare raw data from various sequencing platforms for further analysis, and several bioinformatic applications including sequence annotation and analysis of Pol II binding pattern and histone modification.. The tertiary module for sequence annotation is particularly discussed. xIP-seq also allows users to construct new analysis pipelines tailored for individual biological interests by employing currently available modules or creating new ones. As an example, a “CLIP-seq Mapper” pipeline is created to map CLIP-seq-derived data to human genome to identify the genome-wide annotation of SFRS1 binding pattern. This implementation demonstrates the significance of xIP-seq platform to analyze massive amounts of next-generation sequencing data and provide automatic, flexible, and intelligent enterprise-level bioinformatic solutions.","PeriodicalId":231499,"journal":{"name":"2009 Ohio Collaborative Conference on Bioinformatics","volume":"27 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2009-06-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"121620722","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}

引用次数: 2