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BioStore: A Repository System for Registering and Distributing Public Biology Databases.

Hongseok TAE ; Jeong Min HAN ; Bu Young AHN ; Kiejung PARK

Genomics & Informatics.2009;7(1):49-51.

Although abundant biology data have been accumulated in public biology databases, such as GenBank and PIR, few easy-interface services are provided for users to access or update them. We have developed a system, named BioStore, that is composed of several programs to aid users to not only access public data but also share their own data easily. The service can be used for maintaining a local database as a repository of raw data files of several public databases and distributing the data files to other users. Currently, BioStore manipulates major bio-databases and will expand to include more databases and more useful interfaces.
Biology ; Databases, Nucleic Acid ; Formycins ; Ribonucleotides ; Information Storage and Retrieval

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A Simple Java Sequence Alignment Editing Tool for Resolving Complex Repeat Regions.

Seong Il HAM ; Kyung Eun LEE ; Hyun Seok PARK

Genomics & Informatics.2009;7(1):46-48.

Finishing is the most time-consuming step in sequencing, and many genome projects are left unfinished due to complex repeat regions. Here, we have developed BACContigEditor, a prototype shotgun sequence finishing tool. It is essentially an editor that visualizes assemblies of shotgun sequence fragment reads as gapped multiple alignments. The program offers some flexibility that is needed to rapidly resolve complex regions within a working session. The sole purpose of the release is to promote collaborative creation of extensible software for fragment assembly editors, foster collaborative development, and reduce barriers to initial tool development effort. We describe our software architecture and identify current challenges. The program is available under an Open Source license.
Genome ; Indonesia ; Pliability ; Sequence Alignment

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An Integrated Database and Web Service for Microbial Resources at KACC.

Chang Kug KIM ; Young Ah JEON ; Gyu Taek CHO ; Soon Wo KWON ; Yong Hwan KIM ; Seung Beom HONG

Genomics & Informatics.2009;7(1):41-45.

The Korean Agricultural Culture Collection (KACC) has developed a web-based system to provide an integrated database with information updates about microbial resources. This integrated database consists of 5 major functions and contains general information, which includes identification numbers, culture media composition, image information, DNA sequences, patent information, and general forms for ordering and depositing microorganisms. In 2008, KACC started providing characterization information. KACC maintains 9,801 cultures of microorganisms, including 3,296 strains of bacteria, 4,734 fungi, 784 actinomycetes, 64 yeasts, and 923 others.
Actinobacteria ; Bacteria ; Base Sequence ; Culture Media ; Fungi ; Yeasts

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EST Knowledge Integrated Systems (EKIS): An Integrated Database of EST Information for Research Application.

Dae Won KIM ; Tae Sung JUNG ; Young Sang CHOI ; Seong Hyeuk NAM ; Hyuk Ryul KWON ; Dong Wook KIM ; Han Suk CHOI ; Sang Heang CHOI ; Hong Seog PARK

Genomics & Informatics.2009;7(1):38-40.

The EST Knowledge Integrated System, EKIS (http://ekis.kribb.re.kr), was established as a part of Korea's Ministry of Education, Science and Technology initiative for genome sequencing and application research of the biological model organisms (GEAR) project. The goals of the EKIS are to collect EST information from GEAR projects and make an integrated database to provide transcriptomic and metabolomic information for biological scientists. The EKIS constitutes five independent categories and several retrieval systems in each category for incorporating massive EST data from high-throughput sequencing of 65 different species. Through the EKIS database, scientists can freely access information including BLAST functional annotation as well as Genechip and pathway information for KEGG. By integrating complex data into a framework of existing EST knowledge information, the EKIS provides new insights into specialized metabolic pathway information for an applied industrial material.
Data Mining ; Expressed Sequence Tags ; Genome ; Metabolic Networks and Pathways ; Metabolomics ; Models, Biological

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Choosing Optimal STR Markers for Quality Assurance of Distributed Biomaterials in Biobanking.

Tae Hoon CHUNG ; Heejung LEE ; Mihee LEE ; Jae Pil JEON ; Kisang KIM ; Bok Ghee HAN

Genomics & Informatics.2009;7(1):32-37.

The quality assurance (QA) is of utmost importance in biobanks when archived biomaterials are distributed to biomedical researchers. For sample authentication and cross-contamination detection, the two fundamental elements of QA, STR genotyping is usually utilized. However, the incorporated number of STR markers is highly redundant for biobanking purposes, resulting in time and cost inefficiency. An index to measure the cross-contamination detection capability of an STR marker, the mixture probability (MP), was developed. MP as well as other forensic parameters for STR markers was validated using STR genotyping data on 2328 normal Koreans with the commercial AmpFlSTR kit. For Koreans, 7 STR marker (D2S1338, FGA, D18S51, D8S1179, D13S317, D21S11, vWA) set was sufficient to provide discrimination power of ~10(-10) and cross-contamination detection probability of ~1. Interestingly, similar marker sets were obtained from African Americans, Caucasian Americans, and Hispanic Americans under the same level of discrimination power. Only a small subset of commonly used STR markers is sufficient for QA purposes in biobanks. A procedure for selecting optimal STR markers is outlined using STR genotyping results from normal Korean population.
African Americans ; Biocompatible Materials ; Discrimination (Psychology) ; Hispanic Americans ; Humans ; Microsatellite Repeats

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Bioinformatics Analysis of Hsp20 Sequences in Proteobacteria.

Michelle HEINE ; Sathees B C CHANDRA

Genomics & Informatics.2009;7(1):26-31.

Heat shock proteins are a class of molecular chaperones that can be found in nearly all organisms from Bacteria, Archaea and Eukarya domains. Heat shock proteins experience increased transcription during periods of heat induced osmotic stress and are involved in protein disaggregation and refolding as part of a cell's danger signaling cascade. Heat shock protein, Hsp20 is a small molecular chaperone that is approximately 20kDa in weight and is hypothesized to prevent aggregation and denaturation. Hsp20 can be found in several strains of Proteobacteria, which comprises the largest phyla of the Bacteria domain and also contains several medically significant bacterial strains. Genomic analyses were performed to determine a common evolutionary pattern among Hsp20 sequences in Proteobacteria. It was found that Hsp20 shared a common ancestor within and among the five subclasses of Proteobacteria.This is readily apparent from the amount of sequence similarities within and between Hsp20 protein sequences as well as phylogenetic analysis of sequences from proteobacterial and non-proteobacterial species.
Actinobacteria ; Archaea ; Bacteria ; Computational Biology ; Eukaryota ; Heat-Shock Proteins ; Hot Temperature ; Molecular Chaperones ; Proteins ; Proteobacteria ; Shock

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Interaction between Smoking and the STAB2 Gene in the Severity of Rheumatoid Arthritis.

Jin Young MIN ; Kyoung Bok MIN ; Joohon SUNG ; Sung Il CHO

Genomics & Informatics.2009;7(1):20-25.

Rheumatoid arthritis (RA) is a chronic autoimmune disorder that is characterized by inflammation of the synovial tissue and deterioration of the joint and bone. A recent study reported a potential gene-environment interaction between HLA-DR and smoking. The present study investigated whether a specific gene was related to the association between smoking and the severity of RA (rheumatoid factor levels > 20 IU/ml). We used the resources of the NARAC family collection of GAW 15 databases, and 1139 subjects with RF > 20 IU/ml were included in the current analysis. The linkage panel contained 5858 SNP markers, and 5744 SNPs passed quality control criteria. Linear regression analyses, using PLINK software and generalized estimating equation regression models, were used to test for associations between the SNPs and the severity of RA according to smoking groups. Two major findings were established. First, the severity of RA in smokers was associated with rs703618 (p=6x10(-5)), which lies in the intronic region of the stabilin 2 (STAB2) gene on chromosome 12. Second, there were significant differences in the levels of RF between 'ever smokers' and 'never smokers' according to the rs703618 genotype (G/G, A/G, A/A). We investigated whether a specific gene acts as a mediator between smoking and the severity of RA and found that the STAB2 gene could affect this relationship. Our finding indicates that smoking may mediate RA severity by affecting the expression level of a specific gene.
Arthritis ; Arthritis, Rheumatoid ; Chromosomes, Human, Pair 12 ; Gene-Environment Interaction ; Genotype ; HLA-DR Antigens ; Humans ; Hyaluronic Acid ; Inflammation ; Introns ; Joints ; Linear Models ; Polymorphism, Single Nucleotide ; Quality Control ; Smoke ; Smoking

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Association of Common Vitamin D Receptor Gene Variations with Fracture Risk and Bone Mineral Density in Postmenopausal Korean Population.

Joo Yeon HWANG ; Seung Hun LEE ; Ghi Su KIM ; Jung Min KOH ; Min Jin GO ; Tae Ho KIM ; Jung Min HONG ; Eui Kyun PARK ; Shin Yoon KIM ; Jong Young LEE

Genomics & Informatics.2009;7(1):13-19.

Osteoporosis is characterized by impaired osteogenesis. BMD is a major determinant of bone strength. The role of the VDR gene in predisposition to primary osteoporosis has been recognized. However, population-based case-control studies have been reported controversial results for known candidate genes in an ethnically distinct group. To determine the genetic effects of VDR variants on osteoporosis and BMD, we directly sequenced the VDR gene in 24 unrelated Korean individuals and identified eighteen sequence variants. We investigated the potential involvement of eight SNPs in osteoporosis in postmenopausal women (n = 729). Two SNPs (LD) in intron 2, -5294G > C (rs2238135) and -4817G > A (rs17882443) showed the evidence of association with enhanced BMD of the femoral neck (p(additive) =0.031 for rs2238135; p(additive)=0.017 and p(dominant)= 0.019 for 17882443). Moreover, VDR -4817G > A was significantly associated with protective effect on all fracture risk (p(recessive)=0.035, OR=0.2, 95% CI=0.05~0.89), and tended to be higher BMD values at various proximal femur sites. Therefore, we suggest that the -4817G > A may be useful genetic marker for vitamin D-related metabolism and may have an important role in the increased BMD of the proximal femur in postmenopausal Korean women.
Bone Density ; Case-Control Studies ; Female ; Femur ; Femur Neck ; Genetic Markers ; Humans ; Introns ; Osteogenesis ; Osteoporosis ; Polymorphism, Single Nucleotide ; Receptors, Calcitriol ; Vitamin D ; Vitamins

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An Alternative Way of Constructing Ancestral Graphs Using Marker Allele Ages from Population Linkage Disequilibrium Information.

Leeyoung PARK

Genomics & Informatics.2009;7(1):1-12.

An alternative way of constructing ancestral graphs, which is different from the coalescent-based approach, is proposed using population linkage disequilibrium (LD) data. The main difference from the existing method is the construction of the ancestral graphs based on variants instead of individual sequences. Therefore, the key of the proposed method is to use the order of allele ages in the graphs. Distinct from the previous age-estimation methods, allele ages are estimated from full haplotype information by examining the number of generations from the initial complete LD to the current decayed state for each two variants depending on the direction of LD decay between variants. Using a simple algorithmic procedure, an ancestral graph can be derived from the expected allele ages and current LD decay status. This method is different in many ways from previous methods, and, with further improvement, it might be a good replacement for the current approaches.
Alleles ; Family Characteristics ; Haplotypes ; Linkage Disequilibrium ; Recombination, Genetic

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Comparison of Normalization Methods for Defining Copy Number Variation Using Whole-genome SNP Genotyping Data.

Ji Hong KIM ; Seon Hee YIM ; Yong Bok JEONG ; Seong Hyun JUNG ; Hai Dong XU ; Seung Hun SHIN ; Yeun Jun CHUNG

Genomics & Informatics.2008;6(4):231-234.

Precise and reliable identification of CNV is still important to fully understand the effect of CNV on genetic diversity and background of complex diseases. SNP marker has been used frequently to detect CNVs, but the analysis of SNP chip data for identifying CNV has not been well established. We compared various normalization methods for CNV analysis and suggest optimal normalization procedure for reliable CNV call. Four normal Koreans and NA10851 HapMap male samples were genotyped using Affymetrix Genome-Wide Human SNP array 5.0. We evaluated the effect of median and quantile normalization to find the optimal normalization for CNV detection based on SNP array data. We also explored the effect of Robust Multichip Average (RMA) background correction for each normalization process. In total, the following 4 combinations of normalization were tried: 1) Median normalization without RMA background correction, 2) Quantile normalization without RMA background correction, 3) Median normalization with RMA background correction, and 4) Quantile ormalization with RMA background correction. CNV was called using SW-ARRAY algorithm. We applied 4 different combinations of normalization and compared the effect using intensity ratio profile, box plot, and MA plot. When we applied median and quantile normalizations without RMA background correction, both methods showed similar normalization effect and the final CNV calls were also similar in terms of number and size. In both median and quantile normalizations, RMA background correction resulted in widening the range of intensity ratio distribution, which may suggest that RMA background correction may help to detect more CNVs compared to no correction.
Coat Protein Complex I ; Genetic Variation ; HapMap Project ; Humans ; Male

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