• Genomics & Informatics
• /
• v.2 no.4
• /
• pp.180-183
• /
• 2004

Comparative Statistic Module(CSM) provides more reliable list of significant genes to genomics researchers by offering the commonly selected genes and a method of choice by calculating the rank of each statistical test based on the average ranking of common genes across the five statistical methods, i.e. t-test, Kruskal-Wallis (Wilcoxon signed rank) test, SAM, two sample multiple test, and Empirical Bayesian test. This statistical analysis module is implemented in Perl, and R languages.

• Proceedings of the Korean Society for Bioinformatics Conference
• /
• 2003.10a
• /
• pp.183-192
• /
• 2003

With the availability of complete whole-genomes such as the human, mouse, fugu and chimpanzee chromosome 22, comparative analysis of large genomes from cross-species at varying evolutionary distances is considered one of a powerful approach for identifying coding and functional non-coding sequences. Here we describe a fast and efficient global alignment method especially for large genomic regions over mega bases pair. We used an approach for identifying all similarity regions by HSP (Highest Segment Pair) regions using local alignments and then large syntenic genome based on the both extension of anchors at HSP regions in two species and global conservation map. Using this alignment approach, we examined rearrangement loci in human chromosome 21 and chimpanzee chromosome 22. Finally, we extracted syntenic genome 30 Mb of human chromosome 21 with chimpanzee chromosome 22, and then identified genomic rearrangements (deletions and insertions ranging h size from 0.3 to 200 kb). Our experiment shows that all jnsertion/deletion (indel) events in excess of 300 bp within chimpanzee chromosome 22 and human chromosome 21 alignments in order to identify new insertions that had occurred over the last 7 million years of evolution. Finally we also discussed evolutionary features throughout comparative analyses of Ka/ks (non-synonymous / synonymous substitutions) rate in orthologous 119 genes of chromosome 21 and 53 genes of MHC-I class in human and chimpanzee genome.

• Proceedings of the Korean Society for Bioinformatics Conference
• /
• 2002.06b
• /
• pp.111-123
• /
• 2002

• Proceedings of the Korean Society for Bioinformatics Conference
• /
• 2004.11a
• /
• pp.13-20
• /
• 2004

Grid system has the potential to resolve the current need of bioinformatics for super-computing environment inexpensively. There are already several Grid applications of bioinformatics tools. To solve the real-world bioinformatics problems, however, the various integration of each tool is necessary in addition to the implementation of more basic tools. Workflow based problem solving environment can be the efficient solution for this type of software development. There are still heavy overhead, however, to develop and implement workflow model on current Grid system. He re we propose a model of simple problem solving environment that enables component based workflow design of integrated bioinformatics applications on Grid environment by using Condor functionalities. We realized this model for practical bioinformatics solutions of a genome sequence analysis and a comparative genome analysis. We implemented necessary bioinformatics tools and interfacing tools as the components, and combine them in the workflow model of each solution by using the tools presented in Condor.

• Genomics & Informatics
• /
• v.4 no.4
• /
• pp.147-160
• /
• 2006

GATA transcription factors are widespread eukaryotic regulators whose DNA-binding domain is a class IV zinc finger motif in the form $CX_{2}CX_{17-20}CX_{2}C$followed by a basic region. In fungi, they act as transcriptional activators or repressors in several different processes, ranging from nitrogen source utilization to mating-type switching. Using an in-house bioinformatics portal system, we surveyed 50 fungal and 9 out-group genomes and identified 396 putative fungal GATA transcription factors. The proportion of GATA transcription factors within a genome varied among taxonomic lineages. Subsequent analyses of phylogenetic relationships among the fungal GATA transcription factors, as well as a study of their domain architecture and gene structure, demonstrated high degrees of conservation in type IVa and type IVb zinc finger motifs and the existence of distinctive clusters at least at the level of subphylum. The SFH1 subgroup with a 20-residue loop was newly identified, in addition to six well-defined subgroups in the subphylum Pezizomycotina. Furthermore, a novel GATA motif with a 2f-residue loop ($CX_{2}CX_{21}CX_{2}C$, designated 'zinc finger type IVc') was discovered within the phylum Basidiomycota. Our results suggest that fungal GATA factors might have undergone multiple distinct modes of evolution resulting in diversified cellular modulation in fungi.

• Genomics & Informatics
• /
• v.2 no.3
• /
• pp.147-148
• /
• 2004

Recently completed mitochondrial genome databses from public resources provide us with a better understanding of individual mitochondrial genomes for population genomics. By determining the substitution rate of the genomic sequences, it is plausible to derive dates on the phylogenetic tree and build a chronology of events in the evolution of human species. MitGEN is specially designed as a mitochondrial genome browser for analyzing, comparing and visualizing single nucleotide polymorphism for human mitochondrial genomes between human races for comparative genomics. It is a standalone application and is available free for non-commercial work.

• Proceedings of the Zoological Society Korea Conference
• /
• 2003.08a
• /
• pp.199.2-199
• /
• 2003

No Abstract, See Full Text

• Proceedings of the Zoological Society Korea Conference
• /
• 2003.08a
• /
• pp.198.2-198
• /
• 2003

No Abstract, See Full Text

• Genomics & Informatics
• /
• v.11 no.1
• /
• pp.52-54
• /
• 2013

Proteins in DNAJ/K families are ubiquitous, from prokaryotes to eukaryotes, and function as molecular chaperones. For systematic phylogenomics of the DNAJ/K families, we developed the Eukaryotic DNAJ/K Database (EDD). A total of 12,908 DNAJs and 4,886 DNAKs were identified from 339 eukaryotic genomes in the EDD. Kingdom-wide comparison of DNAJ/K families provides new insights on the evolutionary relationship within these families. Empowered by 'class', 'cluster', and 'taxonomy' browsers and the 'favorite' function, the EDD provides a versatile platform for comparative genomic analyses of DNAJ/K families.

• Journal of Information Management
• /
• v.40 no.1
• /
• pp.157-181
• /
• 2009

As the information technology is evolved and the human genome project is finalized over the world, the Bioinformatics - the integration of abundant Biological science and information technology - has shown up and is continuously being advanced. Together with the evolution of Bioinformatics, the websites dealing with Bioinformation have been set up to provide relevant information to the Bioscientists. Among the numerous global websites, the preferred websites by the majority of domestic Bioscientists are BRIC (Biological Research Information Center) of POSTECH(Pohang University of Science and Technology) in Korea, CCBB(Center for Computational Biology and Bioinformatics) of KISTI(Korea Institute of Science and Technology Information), KOBIC(Korean Bioinformation Center) of KRIBB(Korea Research Institute of Bioscience and Biotechnology), NCBI(National Center for Biotechnology Information) in USA, EBI(European Bioinformatics Institute) in Europe and DDBJ(DNA Data Bank of Japan) in Japan. In this paper, the comparative analysis was executed by investigating contents status and functions of the above-mentioned 6 websites. In addition, questionnaire survey of Bioscience Researchers' utilization status and their needs to those 6 websites was conducted.