Proceedings of the ... Asia-Pacific bioinformatics conference最新文献_第5页

Flow Model of the Protein-protein Interaction Network for Finding Credible Interactions 寻找可信相互作用的蛋白质-蛋白质相互作用网络流模型

Proceedings of the ... Asia-Pacific bioinformatics conference Pub Date : 2007-01-01 DOI: 10.1142/9781860947995_0034

Kinya Okada, K. Asai, Masanori Arita

引用次数: 2

Fast Structural Similarity Search Based on Topology String Matching 基于拓扑字符串匹配的快速结构相似性搜索

Proceedings of the ... Asia-Pacific bioinformatics conference Pub Date : 2007-01-01 DOI: 10.1142/9781860947995_0036

Sung-Hee Park, D. Gilbert, K. Ryu

引用次数: 1

Inferring Gene Regulatory Networks by Machine Learning Methods 用机器学习方法推断基因调控网络

Proceedings of the ... Asia-Pacific bioinformatics conference Pub Date : 2007-01-01 DOI: 10.1142/9781860947995_0027

J. Supper, H. Fröhlich, C. Spieth, Andreas Dräger, A. Zell

引用次数: 6

All Hits All The Time: Parameter Free Calculation of Seed Sensitivity 所有命中所有时间:种子敏感性的参数自由计算

Proceedings of the ... Asia-Pacific bioinformatics conference Pub Date : 2007-01-01 DOI: 10.1142/9781860947995_0035

Denise Y. F. Mak, Gary Benson

{"title":"All Hits All The Time: Parameter Free Calculation of Seed Sensitivity","authors":"Denise Y. F. Mak, Gary Benson","doi":"10.1142/9781860947995_0035","DOIUrl":"https://doi.org/10.1142/9781860947995_0035","url":null,"abstract":"Standard search techniques for DNA repeats start by identifying seeds , that is, small matching words, that may inhabit larger repeats. Recent innovations in seed structure have led to the development of spacedseeds [8] andindel seeds [9] which are more sensitive than contiguous seeds (also known as k-mers, k-tuples, l-words, etc.). Evaluating seed s nsitivityrequires 1) specifying a homology model which describes types of alignments that can occur between two copies of a repeat, and 2) assigning probabilities to those alignments. Optimal seed selection is a resource intensive activity because essentially all alternative seeds must be tested [7]. Current methods require that the model and probability parameters be specified in advance. When the parameters change, the entire calculation has to be rerun. In this paper, we show how to eliminatethe need for prior parameter specification. The ideas presented follow from a simple observation: given a homology model, the alignments hit by a particular seed remain the same regardless of the probability parameters. Only the weights assigned to those alignments change. Therefore, if we know all the hits, we can easily (and quickly) find optimal seeds. We describe a highly efficient preprocessing step, which is computed just oncefor each seed. In this calculation, strings which represent possible alignments are unweightedby any probability parameters. Then we show several increasingly efficient methods to find the optimal seed when given specific probability parameters. Indeed, we show how to determine exactly which seeds can never be optimal under any set of probability parameters. This leads to the startling observation that out of thousands of seeds, only a handful have any chance of being optimal. We then show how to find optimal seeds and the boundaries within probability space where they are optimal. We expect this method to greatly facilitate the study of seed space sensitivity, construction of multiple seed sets, and the use of alternative definitions of optimality.","PeriodicalId":74513,"journal":{"name":"Proceedings of the ... Asia-Pacific bioinformatics conference","volume":"31 1","pages":"327-340"},"PeriodicalIF":0.0,"publicationDate":"2007-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77724482","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: 15

Semi-supervised Pattern Learning for Extracting Relations from Bioscience Texts 生物科学文本关系提取的半监督模式学习

Proceedings of the ... Asia-Pacific bioinformatics conference Pub Date : 2007-01-01 DOI: 10.1142/9781860947995_0033

Shilin Ding, Minlie Huang, Xiaoyan Zhu

引用次数: 5

Exploring Genomes of Distantly Related Mammals 探索近亲哺乳动物的基因组

Proceedings of the ... Asia-Pacific bioinformatics conference Pub Date : 2007-01-01 DOI: 10.1142/9781860947995_0001

J. Graves

{"title":"Exploring Genomes of Distantly Related Mammals","authors":"J. Graves","doi":"10.1142/9781860947995_0001","DOIUrl":"https://doi.org/10.1142/9781860947995_0001","url":null,"abstract":"There are three groups of extant mammals, two of which abound in Australia. Marsupials (kangaroos and their relatives) and monotremes (echidna and the fabulous platypus) have been evolving independently for most of mammalian history. The genomes of marsupial and monotreme mammals are particularly valuable because these alternative mammals fill a phylogenetic gap in vertebrate species lined up for exhaustive genomic study. Human and mice (∼70MY) are too close to distinguish signal, whereas mammal/bird comparisons (∼310MY) are too distant to allow alignment. Kangaroos (180 MY) and platypus (210 MY) are just right. Sequence has diverged sufficiently for stringent detection of homologies that can reveal coding regions and regulatory signals. Importantly, marsupials and monotremes share with humans many mammal-specific developmental pathways and regulatory systems such as sex determination, lactation and X chromosome inactivation. The ARC Centre for Kangaroo Genomics is characterizing the genome of the model Australian kangaroo Macropus eugenii (the tammar wallaby), which is being sequenced by AGRF in Australia, and Baylor (funded by NIH) in the US. We are developing detailed physical and linkage maps of the genome to complement sequencing, and will prepare and array cDNAs for functional studies, especially of reproduction and development. Complete sequencing of the distantly related Brazilian short-tailed opossum Monodelphis domestica by the NIH allows us to compare distantly related marsupials. Sequencing of the genome of the platypus, Ornithorhynchus anatinus by Washington University (funded by the NIH) is complete, and our lab is anchoring contigs to the physical map. We have isolated and completely characterized many BACs and cDNAs containing kangaroo and platypus genes of interest, and demonstrate the value of comparisons to reveal conserved genome organization and function, and new insights in the evolution of the mammalian genome, particularly sex chromosomes.","PeriodicalId":74513,"journal":{"name":"Proceedings of the ... Asia-Pacific bioinformatics conference","volume":"2 1","pages":"1"},"PeriodicalIF":0.0,"publicationDate":"2007-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78925367","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

Deriving Protein Structure Topology from the Helix Skeletion in Low Resolution Density Map using Rosetta 利用Rosetta从低分辨率密度图的螺旋骨架中提取蛋白质结构拓扑

Proceedings of the ... Asia-Pacific bioinformatics conference Pub Date : 2007-01-01 DOI: 10.1142/9781860947995_0017

Y. Lu, Jing He, C. Strauss

{"title":"Deriving Protein Structure Topology from the Helix Skeletion in Low Resolution Density Map using Rosetta","authors":"Y. Lu, Jing He, C. Strauss","doi":"10.1142/9781860947995_0017","DOIUrl":"https://doi.org/10.1142/9781860947995_0017","url":null,"abstract":"Electron cryo-microscopy (cryo-EM) is an experimental technique to determine the 3-dimensional structure for large protein complexes. Currently this technique is able to generate protein density maps at 6 to 9 A resolution. Although secondary structures such as α-helix and β-sheet can be visualized from these maps, there is no mature approach to deduce their tertiary topology, the linear order of the secondary structures on the sequence. The problem is challenging because given N secondary structure elements, the number of possible orders is (2)*N!. We have developed a method to predict the topology of the secondary structures using ab initio structure prediction. The Rosetta structure prediction algorithm was used to make purely sequence based structure predictions for the protein. We produced 1000 of these ab initio models, and then screened the models produced by Rosetta for agreement with the helix skeleton derived from the density map. The method was benchmarked on 60 mainly alpha helical proteins, finding that for about 3/4 of all the proteins, the majority of the helices in the skeleton were correctly assigned by one of the top 10 suggested topologies from the method, while for about 1/3 of all the proteins the best topology assignment without errors was ranked the first. This approach also provides an estimate of the sequence alignment of the skeleton. For most of those true-positive assignments, the alignment was accurate to within +/2 amino acids in the sequence.","PeriodicalId":74513,"journal":{"name":"Proceedings of the ... Asia-Pacific bioinformatics conference","volume":"192 1","pages":"143-151"},"PeriodicalIF":0.0,"publicationDate":"2007-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83024073","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

Combining N-grams and Alignment in G-protein Coupling Specificity Prediction 结合N-grams和比对技术预测g蛋白偶联特异性

Proceedings of the ... Asia-Pacific bioinformatics conference Pub Date : 2007-01-01 DOI: 10.1142/9781860947995_0038

B. Cheng, J. Carbonell

引用次数: 2

Computing the Quartet Distance Between Evolutionary Trees of Bounded Degree 计算有界度进化树之间的四重奏距离

Proceedings of the ... Asia-Pacific bioinformatics conference Pub Date : 2007-01-01 DOI: 10.1142/9781860947995_0013

M. Stissing, Christian N. S. Pedersen, T. Mailund, G. Brodal, Rolf Fagerberg

引用次数: 17

Protein Structure-Structure Alignment with Discrete Fr'echet Distance 蛋白质结构-离散链距离的结构比对

Proceedings of the ... Asia-Pacific bioinformatics conference Pub Date : 2007-01-01 DOI: 10.1142/9781860947995_0016

Minghui Jiang, Ying Xu, B. Zhu

引用次数: 15