IPSJ Transactions on Bioinformatics
Online ISSN : 1882-6679
ISSN-L : 1882-6679
Volume 1
Displaying 1-6 of 6 articles from this issue
  • Tatsuya Akutsu
    Article type: Editorial
    Subject area: Editorial
    2008 Volume 1 Pages 1
    Published: 2008
    Released on J-STAGE: November 28, 2008
    JOURNAL FREE ACCESS
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  • Shinsuke Yamada, Osamu Gotoh, Hayato Yamana
    Article type: Original Papers
    Subject area: Original Paper
    2008 Volume 1 Pages 2-12
    Published: 2008
    Released on J-STAGE: November 28, 2008
    JOURNAL FREE ACCESS
    Multiple sequence alignment (MSA) is a useful tool in bioinformatics. Although many MSA algorithms have been developed, there is still room for improvement in accuracy and speed. We have developed an MSA program PRIME, whose crucial feature is the use of a group-to-group sequence alignment algorithm with a piecewise linear gap cost. We have shown that PRIME is one of the most accurate MSA programs currently available. However, PRIME is slower than other leading MSA programs. To improve computational performance, we newly incorporate anchoring and grouping heuristics into PRIME. An anchoring method is to locate well-conserved regions in a given MSA as anchor points to reduce the region of DP matrix to be examined, while a grouping method detects conserved subfamily alignments specified by phylogenetic tree in a given MSA to reduce the number of iterative refinement steps. The results of BAliBASE 3.0 and PREFAB 4 benchmark tests indicated that these heuristics contributed to reduction in the computational time of PRIME by more than 60% while the average alignment accuracy measures decreased by at most 2%. Additionally, we evaluated the effectiveness of iterative refinement algorithm based on maximal expected accuracy (MEA). Our experiments revealed that when many sequences are aligned, the MEA-based algorithm significantly improves alignment accuracy compared with the standard version of PRIME at the expense of a considerable increase in computation time.
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  • Tomohiro Yasuda
    Article type: Original Papers
    Subject area: Original Paper
    2008 Volume 1 Pages 13-22
    Published: 2008
    Released on J-STAGE: November 28, 2008
    JOURNAL FREE ACCESS
    Let T be a set of hidden strings and S be a set of their concatenations. We address the problem of inferring T from S. Any formalization of the problem as an optimization problem would be computationally hard, because it is NP-complete even to determine whether there exists T smaller than S, and because it is also NP-complete to partition only two strings into the smallest common collection of substrings. In this paper, we devise a new algorithm that infers T by finding common substrings in S and splitting them. This algorithm is scalable and can be completed in O(L)-time regardless of the cardinality of S, where L is the sum of the lengths of all strings in S. In computational experiments, 40, 000 random concatenations of randomly generated strings were successfully decomposed, as well as the effectiveness of our method for this problem was compared with that of multiple sequence alignment programs. We also present the result of a preliminary experiment against the transcriptome of Homo sapiens and describe problems in applications where real large-scale cDNA sequences are analyzed.
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  • Tatsuya Akutsu, Morihiro Hayashida, Shu-Qin Zhang, Wai-Ki Ching, Micha ...
    Article type: Original Papers
    Subject area: Original Paper
    2008 Volume 1 Pages 23-34
    Published: 2008
    Released on J-STAGE: November 28, 2008
    JOURNAL FREE ACCESS
    We study the predecessor and control problems for Boolean networks (BNs). The predecessor problem is to determine whether there exists a global state that transits to a given global state in a given BN, and the control problem is to find a sequence of 0-1 vectors for control nodes in a given BN which leads the BN to a desired global state. The predecessor problem is useful both for the control problem for BNs and for analysis of landscape of basins of attractions in BNs. In this paper, we focus on BNs of bounded indegree and show some hardness results on the computational complexity of the predecessor and control problems. We also present simple algorithms for the predecessor problem that are much faster than the naive exhaustive search-based algorithm. Furthermore, we show some results on distribution of predecessors, which leads to an improved algorithm for the control problem for BNs of bounded indegree.
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  • Hisamitsu Akiba, Y-h. Taguchi
    Article type: Original Papers
    Subject area: Original Paper
    2008 Volume 1 Pages 35-41
    Published: 2008
    Released on J-STAGE: November 28, 2008
    JOURNAL FREE ACCESS
    The Barcode of Life (BOL) project aims to identify species with no other information than DNA sequence. We assume that BOL includes information on higher taxa. In the present study, we compute nonmetric distance from BOL barcodes by using rank order of pairwise distance for 3 distinct examples, namely, Ant Diversity in Northern Madagascar, Survey of Chelicerates, and Birds of North America. This enables us to recognize higher taxa, i.e., genus, family, and order, more easily. For example, the ratio of mean inner taxa nonmetric distance to the intertaxa distance is smaller than that for raw (metric) distance. Furthermore, for most pairs of higher taxa, the mean intertaxa distance is more than twice larger than intrataxa distances. The nonmetric multidimensional scaling method enables to discriminate higher taxa compared to tree construction by the neighbor-joining method or the maximum parsimony method with raw distance measure, when each species is embedded into more than 40 dimensional space with an accuracy of 90% even after leave-one-out-cross-validation.
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  • Susumu Date, Kazunori Nozaki, Haruki Nakamura, Saburo Sakoda, Shinji S ...
    Article type: Original Papers
    Subject area: Original Paper
    2008 Volume 1 Pages 42-52
    Published: 2008
    Released on J-STAGE: November 28, 2008
    JOURNAL FREE ACCESS
    The Grid has increasingly gathered the attention and interest of scientists and researchers as a building block technology for computational infrastructure. Because of the recent increasing demands on the Grid, the utilization of the Grid has been explored in various scientific research areas. In reality, however, the Grid is not fully utilized well in today's practical scientific research areas treating security-sensitive data, especially in biomedical research areas. This is partly due to the lack of know-how about how access control can be achieved in the actual applications despite the maturity of security technologies related to authentication and authorization. From this perspective, in this paper, we present a Grid-aware access control mechanism leveraging MyProxy, GSI, PERMIS and XSLT, which we have built into a clinical database for Parkinson's research and diagnosis. In particular, we focus on how these technologies are used to satisfy the access control requirements derived from a clinical database. Also, it is shown that the proposed access control mechanism can be operated with low-cost administration and acceptable overhead.
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