• Journal of the Korea Society of Computer and Information
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• v.3 no.1
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• pp.25-34
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• 1998

There are two major method for expressing parallelim in functional languages. The one is the strictness analysis and the other the annotation. The strictness analysis is a method that a compiler detects parallelism and expresses the detected information in the object program. The annotation is a method that a programmer detects parallelism and expresses in the source program. This study is on the annotation and is aimed at construction of a translator for a functional language which has an annotation syntax. The translator translates a source program to enriched lambda-calculus graphs. The translator is implemented in C using compiler development tools such as YACC and Lex, under UNIX environments. In this paper we present the design and implementation techniques for developing the front-end of the translator.

• Genomics & Informatics
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• v.12 no.2
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• pp.76-78
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• 2014

Owing to the generation of vast amounts of sequencing data by using cost-effective, high-throughput sequencing technologies with improved computational approaches, many putative proteins have been discovered after assembly and structural annotation. Putative proteins are typically annotated using a functional annotation system that uses extant databases, but the expansive size of these databases often causes a bottleneck for rapid functional annotation. We developed SFannotation, a simple and fast functional annotation system that rapidly annotates putative proteins against four extant databases, Swiss-Prot, TIGRFAMs, Pfam, and the non-redundant sequence database, by using a best-hit approach with BLASTP and HMMSEARCH.

• Genomics & Informatics
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• v.19 no.4
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• pp.43.1-43.12
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• 2021

Campylobacter jejuni is one of the most prevalent organisms associated with foodborne illness across the globe causing campylobacteriosis and gastritis. Many proteins of C. jejuni are still unidentified. The purpose of this study was to determine the structure and function of a non-annotated hypothetical protein (HP) from C. jejuni. A number of properties like physiochemical characteristics, 3D structure, and functional annotation of the HP (accession No. CAG2129885.1) were predicted using various bioinformatics tools followed by further validation and quality assessment. Moreover, the protein-protein interactions and active site were obtained from the STRING and CASTp server, respectively. The hypothesized protein possesses various characteristics including an acidic pH, thermal stability, water solubility, and cytoplasmic distribution. While alpha-helix and random coil structures are the most prominent structural components of this protein, most of it is formed of helices and coils. Along with expected quality, the 3D model has been found to be novel. This study has identified the potential role of the HP in 2-methylcitric acid cycle and propionate catabolism. Furthermore, protein-protein interactions revealed several significant functional partners. The in-silico characterization of this protein will assist to understand its molecular mechanism of action better. The methodology of this study would also serve as the basis for additional research into proteomic and genomic data for functional potential identification.

• Journal of Animal Science and Technology
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• v.65 no.2
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• pp.293-310
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• 2023

Protein-translated mRNA analysis has been extensively used to determine the function of various traits in animals. The non-coding RNA (ncRNA), which was known to be non-functional because it was not encoded as a protein, was re-examined as it was studied to actually function. One of the ncRNAs, long non-coding RNA (lncRNA), is known to have a function of regulating mRNA expression, and its importance is emerging. Therefore, lncRNAs are currently being used to understand the traits of various animals as well as human diseases. However, studies on lncRNA annotation and its functions are still lacking in most animals except humans and mice. lncRNAs have unique characteristics of lncRNAs and interact with mRNA through various mechanisms. In order to make lncRNA annotations in animals in the future, it is essential to understand the characteristics of lncRNAs and the mechanisms by which lncRNAs function. In addition, this will allow lncRNAs to be used for a wider variety of traits in a wider range of animals, and it is expected that integrated analysis using other biological information will be possible.

• Genomics & Informatics
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• v.17 no.4
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• pp.46.1-46.7
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• 2019

The implications of germline de novo variants (DNVs) in diseases are well documented. Despite extensive research, inconsistencies between studies remain a challenge, and the distribution and genetic characteristics of DNVs need to be precisely evaluated. To address this issue at the whole-genome scale, a large number of DNVs identified from the whole-genome sequencing of 1,902 healthy trios (i.e., parents and progeny) from the Simons Foundation for Autism Research Initiative study and 20 healthy Korean trios were analyzed. These apparently nonpathogenic DNVs were enriched in functional elements of the genome but relatively depleted in regions of common copy number variants, implying their potential function as triggers of evolution even in healthy groups. No strong mutational hotspots were identified. The pathogenicity of the DNVs was not strongly elevated, reflecting the health status of the cohort. The mutational signatures were consistent with previous studies. This study will serve as a reference for future DNV studies.

• Genomics & Informatics
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• v.19 no.1
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• pp.3.1-3.12
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• 2021

Functional interpretation of noncoding genetic variants associated with complex human diseases and traits remains a challenge. In an effort to enhance our understanding of common germline variants associated with lung cancer, we categorize regulatory elements based on eight major cell types of human lung tissue. Our results show that 21.68% of lung cancer-associated risk variants are linked to noncoding regulatory elements, nearly half of which are cell type-specific. Integrative analysis of high-resolution long-range chromatin interactome maps and single-cell RNA-sequencing data of lung tumors uncovers number of putative target genes of these variants and functionally relevant cell types, which display a potential biological link to cancer susceptibility. The present study greatly expands the scope of functional annotation of lung cancer-associated genetic risk factors and dictates probable cell types involved in lung carcinogenesis.

• Genomics & Informatics
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• v.21 no.2
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• pp.21.1-21.14
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• 2023

Fusobacterium nucleatum is a gram-negative bacteria associated with diverse infections like appendicitis and colorectal cancer. It mainly attacks the epithelial cells in the oral cavity and throat of the infected individual. It has a single circular genome of 2.7 Mb. Many proteins in F. nucleatum genome are listed as "Uncharacterized." Annotation of these proteins is crucial for obtaining new facts about the pathogen and deciphering the gene regulation, functions, and pathways along with discovery of novel target proteins. In the light of new genomic information, an armoury of bioinformatic tools were used for predicting the physicochemical parameters, domain and motif search, pattern search, and localization of the uncharacterized proteins. The programs such as receiver operating characteristics determine the efficacy of the databases that have been employed for prediction of different parameters at 83.6%. Functions were successfully assigned to 46 uncharacterized proteins which included enzymes, transporter proteins, membrane proteins, binding proteins, etc. Apart from the function prediction, the proteins were also subjected to string analysis to reveal the interacting partners. The annotated proteins were also put through homology-based structure prediction and modeling using Swiss PDB and Phyre2 servers. Two probable virulent factors were also identified which could be investigated further for potential drug-related studies. The assigning of functions to uncharacterized proteins has shown that some of these proteins are important for cell survival inside the host and can act as effective drug targets.

• Journal of Animal Science and Technology
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• v.57 no.12
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• pp.44.1-44.9
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• 2015

Background: Heat shock proteins play an important role in protection from stress stimuli and metabolic insults in almost all organisms. Methods: In this study, computational tools were used to deeply analyse the physicochemical characteristics and, using homology modelling, reliably predict the tertiary structure of the blunt snout bream (Ma-) Hsp70 and Hsc70 proteins. Derived three-dimensional models were then used to predict the function of the proteins. Results: Previously published predictions regarding the protein length, molecular weight, theoretical isoelectric point and total number of positive and negative residues were corroborated. Among the new findings are: the extinction coefficient (33725/33350 and 35090/34840 - Ma-Hsp70/ Ma-Hsc70, respectively), instability index (33.68/35.56 - both stable), aliphatic index (83.44/80.23 - both very stable), half-life estimates (both relatively stable), grand average of hydropathicity (-0.431/-0.473 - both hydrophilic) and amino acid composition (alanine-lysine-glycine/glycine-lysine-aspartic acid were the most abundant, no disulphide bonds, the N-terminal of both proteins was methionine). Homology modelling was performed by SWISS-MODEL program and the proposed model was evaluated as highly reliable based on PROCHECK's Ramachandran plot, ERRAT, PROVE, Verify 3D, ProQ and ProSA analyses. Conclusions: The research revealed a high structural similarity to Hsp70 and Hsc70 proteins from several taxonomically distant animal species, corroborating a remarkably high level of evolutionary conservation among the members of this protein family. Functional annotation based on structural similarity provides a reliable additional indirect evidence for a high level of functional conservation of these two genes/proteins in blunt snout bream, but it is not sensitive enough to functionally distinguish the two isoforms.

• BMB Reports
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• v.43 no.2
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• pp.79-90
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• 2010

Mouse models are crucial for the functional annotation of human genome. Gene modification techniques including gene targeting and gene trap in mouse have provided powerful tools in the form of genetically engineered mice (GEM) for understanding the molecular pathogenesis of human diseases. Several international consortium and programs are under way to deliver mutations in every gene in mouse genome. The information from studying these GEM can be shared through international collaboration. However, there are many limitations in utility because not all human genes are knocked out in mouse and they are not yet phenotypically characterized by standardized ways which is required for sharing and evaluating data from GEM. The recent improvement in mouse genetics has now moved the bottleneck in mouse functional genomics from the production of GEM to the systematic mouse phenotype analysis of GEM. Enhanced, reproducible and comprehensive mouse phenotype analysis has thus emerged as a prerequisite for effectively engaging the phenotyping bottleneck. In this review, current information on systematic mouse phenotype analysis and an issue-oriented perspective will be provided.

• Proceedings of the Plant Resources Society of Korea Conference
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• 2019.04a
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• pp.35-35
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• 2019

Aster spathulifolius Maxim. is belongs to the Asteraceae family which is distributed only in Korea and Japan. It is recognize as a traditionally medicinal plants and economically valuable in ornamental field. However, among the Asteraceae family, the Aster genus, which is lacks in genomic resources and information of molecular function. Therefore, we used high throughput RNA-sequencing transcriptome data of the A. spathulifolius to know molecular level function. DeNovo assembly produced 98,660 unigene with N50 value 1126 bp. Unigenes was performed to analyses the functional annotation against NCBI database like plant database of nucleotide (Nt) and non-redundant protein (Nr), Pfam, Uniprot, KEGG and Transcriptional factor (TF). In addition, Distribution of SSR markers also analyzed for future perfectives. Further, Comparing with other two Asteraceae family species like, Karelinia caspica and Chrysanthemum morifolium to the A. spathulifolius shows the number of gene that regulated in internal and external stress respectively salt-tolerant and heat and drought stress to understand the molecular basis related to the different environments stress.