Genome informatics. International Conference on Genome Informatics最新文献_第10页

Comprehensive analysis of sequence-structure relationships in the loop regions of proteins. 蛋白质环区序列结构关系的综合分析。

Genome informatics. International Conference on Genome Informatics Pub Date : 2009-10-01 DOI: 10.1142/9781848165632_0010

Shugo Nakamura, K. Shimizu

{"title":"Comprehensive analysis of sequence-structure relationships in the loop regions of proteins.","authors":"Shugo Nakamura, K. Shimizu","doi":"10.1142/9781848165632_0010","DOIUrl":"https://doi.org/10.1142/9781848165632_0010","url":null,"abstract":"Local sequence-structure relationships in the loop regions of proteins were comprehensively estimated using simple prediction tools based on support vector regression (SVR). End-to-end distance was selected as a rough structural property of fragments, and the end-to-end distances of an enormous number of loop fragments from a wide variety of protein folds were directly predicted from sequence information by using SVR. We found that our method was more accurate than random prediction for predicting the structure of fragments comprising 5, 9, and 17 amino acids; moreover, the extended loop fragments could be successfully distinguished from turn structures on the basis of their sequences, which implies that the sequence-structure relationships were significant for loop fragments with a wide range of end-to-end distances. These results suggest that many loop regions as well as helices and strands restrict the conformational space of the entire tertiary structure of proteins to some extent; moreover, our findings throw light on the mechanism of protein folding and prediction of the tertiary structure of proteins without using structural templates.","PeriodicalId":73143,"journal":{"name":"Genome informatics. International Conference on Genome Informatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2009-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81070373","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

An assessment of prediction algorithms for nucleosome positioning. 核小体定位预测算法的评估。

Genome informatics. International Conference on Genome Informatics Pub Date : 2009-10-01 DOI: 10.1142/9781848165632_0016

Yoshiaki Tanaka, K. Nakai

{"title":"An assessment of prediction algorithms for nucleosome positioning.","authors":"Yoshiaki Tanaka, K. Nakai","doi":"10.1142/9781848165632_0016","DOIUrl":"https://doi.org/10.1142/9781848165632_0016","url":null,"abstract":"Nucleosome configuration in eukaryotic genomes is an important clue to clarify the mechanisms of regulation for various nuclear events. In the past few years, numerous computational tools have been developed for the prediction of nucleosome positioning, but there is no third-party benchmark about their performance. Here we present a performance evaluation using genome-scale in vivo nucleosome maps of two vertebrates and three invertebrates. In our measurement, two recently updated versions of Segal's model and Gupta's SVM with the RBF kernel, which was not implemented originally, showed higher prediction accuracy although their performances differ significantly in the prediction of medaka fish and candida yeast. The cross-species prediction results using Gupta's SVM also suggested rather specific characters of nucleosomal DNAs in medaka and budding yeast. With the analyses for over- and under-representat ion of DNA oligomers, we found both general and species-specific motifs in nucleosomal and linker DNAs. The oligomers commonly enriched in all five eukaryotes were only CA/TG and AC/GT. Thus, to achieve relatively high performance for a species, it is desirable to prepare the training data from the same species.","PeriodicalId":73143,"journal":{"name":"Genome informatics. International Conference on Genome Informatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2009-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81566854","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: 16

A new generation of homology search tools based on probabilistic inference. 基于概率推理的新一代同源搜索工具。

Genome informatics. International Conference on Genome Informatics Pub Date : 2009-10-01 DOI: 10.1142/9781848165632_0019

S. Eddy

{"title":"A new generation of homology search tools based on probabilistic inference.","authors":"S. Eddy","doi":"10.1142/9781848165632_0019","DOIUrl":"https://doi.org/10.1142/9781848165632_0019","url":null,"abstract":"Many theoretical advances have been made in applying probabilistic inference methods to improve the power of sequence homology searches, yet the BLAST suite of programs is still the workhorse for most of the field. The main reason for this is practical: BLAST's programs are about 100-fold faster than the fastest competing implementations of probabilistic inference methods. I describe recent work on the HMMER software suite for protein sequence analysis, which implements probabilistic inference using profile hidden Markov models. Our aim in HMMER3 is to achieve BLAST's speed while further improving the power of probabilistic inference based methods. HMMER3 implements a new probabilistic model of local sequence alignment and a new heuristic acceleration algorithm. Combined with efficient vector-parallel implementations on modern processors, these improvements synergize. HMMER3 uses more powerful log-odds likelihood scores (scores summed over alignment uncertainty, rather than scoring a single optimal alignment); it calculates accurate expectation values (E-values) for those scores without simulation using a generalization of Karlin/Altschul theory; it computes posterior distributions over the ensemble of possible alignments and returns posterior probabilities (confidences) in each aligned residue; and it does all this at an overall speed comparable to BLAST. The HMMER project aims to usher in a new generation of more powerful homology search tools based on probabilistic inference methods.","PeriodicalId":73143,"journal":{"name":"Genome informatics. International Conference on Genome Informatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2009-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73217004","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: 1178

Thinking laterally about genomes. 从侧面思考基因组。

Genome informatics. International Conference on Genome Informatics Pub Date : 2009-10-01

Mark A Ragan

{"title":"Thinking laterally about genomes.","authors":"Mark A Ragan","doi":"","DOIUrl":"","url":null,"abstract":"Perhaps the most-surprising discovery of the genome era has been the extent to which prokaryotic and many eukaryotic genomes incorporate genetic material from sources other than their parent(s). Lateral genetic transfer (LGT) among bacteria was first observed about 100 years ago, and is now accepted to underlie important phenomena including the spread of antibiotic resistance and ability to degrade xenobiotics. LGT is invoked, perhaps too readily, to explain a breadth of awkward data including compositional heterogeneity of genomes, disagreement among gene-sequence trees, and mismatch between physiology and systematics. At the same time many details of LGT remain unknown or controversial, and some key questions have scarcely been asked. Here I critically review what we think we know about the existence, extent, mechanism and impact of LGT; identify important open questions; and point to research directions that hold particular promise for elucidating the role of LGT in genome evolution. Evidence for LGT in nature is not only inferential but also direct, and potential vectors are ubiquitous. Genetic material can pass between diverse habitats and be significantly altered during residency in viruses, complicating the inference of donors, In prokaryotes about twice as many genes are interrupted by LGT as are transferred intact, and about 5Short protein domains can be privileged units of transfer. Unresolved phylogenetic issues include the correct null hypothesis, and genes as units of analysis. Themes are beginning to emerge regarding the effect of LGT on cellular networks, but I show why generalization is premature. LGT can associate with radical changes in physiology and ecological niche. Better quantitative models of genome evolution are needed, and theoretical frameworks remain to be developed for some observations including chromosome assembly by LGT.","PeriodicalId":73143,"journal":{"name":"Genome informatics. International Conference on Genome Informatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2009-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28733806","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

The prediction of local modular structures in a co-expression network based on gene expression datasets. 基于基因表达数据集的共表达网络局部模块化结构预测。

Genome informatics. International Conference on Genome Informatics Pub Date : 2009-10-01

Yoshiyuki Ogata, Nozomu Sakurai, Hideyuki Suzuki, Koh Aoki, Kazuki Saito, Daisuke Shibata

{"title":"The prediction of local modular structures in a co-expression network based on gene expression datasets.","authors":"Yoshiyuki Ogata, Nozomu Sakurai, Hideyuki Suzuki, Koh Aoki, Kazuki Saito, Daisuke Shibata","doi":"","DOIUrl":"","url":null,"abstract":"In scientific fields such as systems biology, evaluation of the relationship between network members (vertices) is approached using a network structure. In a co-expression network, comprising genes (vertices) and gene-to-gene links (edges) representing co-expression relationships, local modular structures with tight intra-modular connections include genes that are co-expressed with each other. For detecting such modules from among the whole network, an approach to evaluate network topology between modules as well as intra-modular network topology is useful. To detect such modules, we combined a novel inter-modular index with network density, the representative intra-modular index, instead of a single use of network density. We designed an algorithm to optimize the combinatory index for a module and applied it to Arabidopsis co-expression analysis. To verify the relation between modules obtained using our algorithm and biological knowledge, we compared it to the other tools for co-expression network analyses using the KEGG pathways, indicating that our algorithm detected network modules representing better associations with the pathways. It is also applicable to a large dataset of gene expression profiles, which is difficult to calculate in a mass.","PeriodicalId":73143,"journal":{"name":"Genome informatics. International Conference on Genome Informatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2009-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28735857","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

A method for efficient execution of bioinformatics workflows. 一种有效执行生物信息学工作流程的方法。

Genome informatics. International Conference on Genome Informatics Pub Date : 2009-10-01

Junya Seo, Yoshiyuki Kido, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda

引用次数: 0

Quality control and reproducibility in DNA microarray experiments. DNA微阵列实验的质量控制和可重复性。

Genome informatics. International Conference on Genome Informatics Pub Date : 2009-10-01 DOI: 10.1142/9781848165632_0003

André Fujita, J. Sato, Fernando H L DA Silva, Maria C Galvão, M. Sogayar, S. Miyano

引用次数: 2

Cancer classification using single genes. 使用单基因进行癌症分类。

Genome informatics. International Conference on Genome Informatics Pub Date : 2009-10-01 DOI: 10.1142/9781848165632_0017

Xiaosheng Wang, O. Gotoh

引用次数: 27

Cancer classification using single genes. 使用单基因进行癌症分类。

Genome informatics. International Conference on Genome Informatics Pub Date : 2009-10-01

Xiaosheng Wang, Osamu Gotoh

引用次数: 0

Localized suffix array and its application to genome mapping problems for paired-end short reads. 局部后缀阵列及其在配对短读基因组定位中的应用。

Genome informatics. International Conference on Genome Informatics Pub Date : 2009-10-01

Kouichi Kimura, Asako Koike

{"title":"Localized suffix array and its application to genome mapping problems for paired-end short reads.","authors":"Kouichi Kimura, Asako Koike","doi":"","DOIUrl":"","url":null,"abstract":"We introduce a new data structure, a localized suffix array, based on which occurrence information is dynamically represented as the combination of global positional information and local lexicographic order information in text search applications. For the search of a pair of words within a given distance, many candidate positions that share a coarse-grained global position can be compactly represented in term of local lexicographic orders as in the conventional suffix array, and they can be simultaneously examined for violation of the distance constraint at the coarse-grained resolution. Trade-off between the positional and lexicographical information is progressively shifted towards finer positional resolution, and the distance constraint is reexamined accordingly. Thus the paired search can be efficiently performed even if there are a large number of occurrences for each word. The localized suffix array itself is in fact a reordering of bits inside the conventional suffix array, and their memory requirements are essentially the same. We demonstrate an application to genome mapping problems for paired-end short reads generated by new-generation DNA sequencers. When paired reads are highly repetitive, it is time-consuming to naïvely calculate, sort, and compare all of the coordinates. For a human genome re-sequencing data of 36 base pairs, more than 10 times speedups over the naïve method were observed in almost half of the cases where the sums of redundancies (number of individual occurrences) of paired reads were greater than 2,000.","PeriodicalId":73143,"journal":{"name":"Genome informatics. International Conference on Genome Informatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2009-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28734942","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