IPSJ Transactions on Bioinformatics
Online ISSN : 1882-6679
ISSN-L : 1882-6679
Volume 4
Displaying 1-5 of 5 articles from this issue
  • Tetsuo Shibuya
    Article type: Preface
    Subject area: Preface
    2011 Volume 4 Pages 1
    Published: 2011
    Released on J-STAGE: January 25, 2011
    JOURNAL FREE ACCESS
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  • Akito Taneda
    Article type: Database/Software Papers
    Subject area: Database/Software Paper
    2011 Volume 4 Pages 2-8
    Published: 2011
    Released on J-STAGE: January 25, 2011
    JOURNAL FREE ACCESS
    The importance of non-coding RNAs and their informatics tools has grown for a decade due to a drastic increase of known non-coding RNAs. RNA sequence alignment is one of the most important technologies in such informatics tools. Recently, we have proposed a multi-objective genetic algorithm, Cofolga2mo, for obtaining an approximate set of weak Pareto optimal solutions for global pairwise RNA sequence alignment, where a sequence similarity and a secondary structure contribution are taken into account as objective functions. In the present study, we have developed a web server for obtaining RNA sequence alignments by Cofolga2mo and for assisting the decision making from the alignments. Furthermore, we introduced an index for reducing the number of alignments output by Cofolga2mo. As a result, we successfully reduced the maximum number of alignments for an input RNA sequence pair from fifty to ten without a significant loss of accurate alignments. By using the BRAliBase 2.1 benchmark dataset, we show that a set of alignments output by Cofolga2mo for an input RNA sequence pair, which has at most ten alignments, includes an accurate alignment compared to those of the previous mono-objective RNA sequence alignment programs.
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  • Taiki Miyanishi, Kazuhiro Seki, Kuniaki Uehara
    Article type: Original Papers
    Subject area: Original Paper
    2011 Volume 4 Pages 9-20
    Published: 2011
    Released on J-STAGE: May 18, 2011
    JOURNAL FREE ACCESS
    Accelerated by the technological advances in the biomedical domain, the size of its literature has been growing very rapidly. As a consequence, it is not feasible for individual researchers to comprehend and synthesize all the information related to their interests. Therefore, it is conceivable to discover hidden knowledge, or hypotheses, by linking fragments of information independently described in the literature. In fact, such hypotheses have been reported in the literature mining community; some of which have even been corroborated by experiments. This paper mainly focuses on hypothesis ranking and investigates an approach to identifying reasonable ones based on semantic similarities between events which lead to respective hypotheses. Our assumption is that hypotheses generated from semantically similar events are more reasonable. We developed a prototype system called, Hypothesis Explorer, and conducted evaluative experiments through which the validity of our approach is demonstrated in comparison with those based on term frequencies, often adopted in the previous work.
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  • Wisnu Ananta Kusuma, Takashi Ishida, Yutaka Akiyama
    Article type: Original Papers
    Subject area: Original Paper
    2011 Volume 4 Pages 21-33
    Published: 2011
    Released on J-STAGE: November 04, 2011
    JOURNAL FREE ACCESS
    De novo DNA sequence assembly is very important in genome sequence analysis. In this paper, we investigated two of the major approaches for de novo DNA sequence assembly of very short reads: overlap-layout-consensus (OLC) and Eulerian path. From that investigation, we developed a new assembly technique by combining the OLC and the Eulerian path methods in a hierarchical process. The contigs yielded by these two approaches were treated as reads and were assembled again to yield longer contigs. We tested our approach using three real very-short-read datasets generated by an Illumina Genome Analyzer and four simulated very-short-read datasets that contained sequencing errors. The sequencing errors were modeled based on Illumina's sequencing technology. As a result, our combined approach yielded longer contigs than those of Edena (OLC) and Velvet (Eulerian path) in various coverage depths and was comparable to SOAPdenovo, in terms of N50 size and maximum contig lengths. The assembly results were also validated by comparing contigs that were produced by assemblers with their reference sequence from an NCBI database. The results show that our approach produces more accurate results than Velvet, Edena, and SOAPdenovo alone. This comparison indicates that our approach is a viable way to assemble very short reads from next generation sequencers.
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  • Takahiro Shinozaki, Toshinao Iwaki, Shiqiao Du, Masakazu Sekijima, Sad ...
    Article type: Original Papers
    Subject area: Original Paper
    2011 Volume 4 Pages 34-44
    Published: 2011
    Released on J-STAGE: December 14, 2011
    JOURNAL FREE ACCESS
    Three-dimensional structure prediction of a molecule can be modeled as a minimum energy search problem in a potential landscape. Popular ab initio structure prediction approaches based on this formalization are the Monte Carlo methods represented by the Metropolis method. However, their prediction performance degrades for larger molecules such as proteins since the search space is exponential to the number of atoms. In order to search the exponential space more efficiently, we propose a new method modeling the potential landscape as a factor graph. The key ideas are slicing the factor graph based on the maximum distance of bonded atoms to convert it to a linear structured graph, and the utilization of the max-sum search algorithm combined with samplings. It is referred to as Slice Chain Max-Sum and it has an advantage that the search is efficient because the graph is linear. Experiments are performed using polypeptides having 50 to 300 amino acid residues. It has been shown that the proposed method is computationally more efficient than the Metropolis method for large molecules.
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