Biomedical subjects

Makihiko Sato

Publications and source records attributed to Makihiko Sato.

3 recordsLinked to original sources

PubMed2004

ASIAN: a website for network inference.

UNLABELLED: We constructed a website for inferring a network by applying the graphical Gaussian model, from a large amount of data, including redundant information. The available tools on the website are based on a system, named ASIAN (Automatic System for Inferring A Network), in combination with the two methods in our previous papers, which were designed to analyze gene expression profiles on a genomic scale. One of the remarkable features of the website is its ability to infer a network, concomitant with hierarchical clustering and the following estimation of cluster boundaries. AVAILABILITY: http://eureka.ims.u-tokyo.ac.jp/asian

Computer Simulation↗

PubMed2004

Detection of inter-spread repeat sequence in genomic DNA sequence.

Various types of periodic patterns in nucleotide sequences are known to be very abundant in a genomic DNA sequence, and to play important biological roles such as gene expression, genome structural stabilization, and recombination. We present a new method, named "STEPSTONE", to find a specific periodic pattern of repeat sequence, inter-spread repeat, in which the tandem repeats of the conserved and the not-conserved regions appear periodically. In our method, at first, the data on periods of short repeat sequences found in a target sequence are stored as a hash data, and then are selected by application of an auto-correlation test in time series analysis. Among the statistically selected sequences, the inter-spread repeats are obtained by usual alignment procedures through two steps. To test the performance of our method, we examined the inter-spread repeats in Mycobacterium tuberculosis and Zamia paucijuga genomic sequences. As a result, our method exactly detected the repeats in the two sequences, being useful for identifying systematically the inter-spread repeats in DNA sequence.

Algorithms↗

PubMed2004

Causes for the large genome size in a cyanobacterium Anabaena sp. PCC7120.

Three possible causes responsible for the large genome size of a cyanobacterium Anabaena sp. PCC7120 are investigated: 1) sequential tandem duplications of gene segments, genes or genomic segments, 2) horizontal gene transfers from other organisms, and 3) whole-genome duplication. We evaluated the frequency distribution of angles between paralog locations for the possibility 1), the fraction of genes deviated in GC content, GC skew, AT skew and codon adaptation index for the 2) and the gene-configuration comparison of paralogs for the 3). As a result, the possibility 3), the whole-genome duplication, was more reasonable as a molecular cause than the other causes for the large genome size in Anabaena sp. PCC7120. In addition, the whole-genome duplication was supported by the analysis of distribution pattern of protein genes with respect to functional categories.

Anabaena↗