• Journal of Life Science
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• v.9 no.2
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• pp.9-14
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• 1999

Pseudomonas iodinum IFO 3558 adenosine deaminase(ADA) gene was cloned by the polymerase chain reaction and deduced the amino acid sequence of the enzyme. DNA sequence homology of Pseudomonas iodinum IFO 3558 ADA gene was compared to those of E. coli, human and mouse ADA genes. Unambiguous sequence from both strands of pM21 was obtained for the region believed to encode ADA. The sequence included a 804-nucleotide open reading frame, bounded on one end by sense primer and on the other end by two antisense primer. This open reading frame encodes a protein of 268 amino acids having a molecular weight of 29,448. The deduced amino acid sequence shows considerable similarity to those of E. coli, mouse and human ADA. Pseudomonas iodinum IFO 3558 nucleotide sequence shows 98.5% homology with that of the E. coli ADA sequence and 51.7% homology with that of the mouse ADA sequence and 52.5% homology with that of the human ADA sequence. The ADA protein sequence of Pseudomonas iodinum IFO 3558 shows 96.9% homology with that of the E. coli and 40.7% homology with that of the mouse and 41.8% homology with that of the human. The distance between two of the conserved elements, TVHAGE and SL(1)NTDDP has veen exactly conserved at 76 amino acids for all four ADAs. Two of the four conserved sequence elements shared among the four ADAs are also present in the yeast, rat, human (M), and Human(L) AMP deaminase. The SLSTDDP sequence differs only in the conservative substitution of a serine for an asparagine. A conserved cysteine with conserved spacing between these two regions is also found. Thus, sequence analysis of four ADAs and four AMP deaminases revealed the presence of a highly conserved sequence motif, SLN(S)TDDP, a conserved dipeptide, HA, and a conserved cysteine residue.

• Interdisciplinary Bio Central
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• v.3 no.4
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• pp.14.1-14.9
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• 2011

Protein homology detection is an important issue in comparative genomics. Because of the exponential growth of sequence databases, fast and efficient homology detection tools are urgently needed. Currently, for homology detection, sequence comparison methods using local alignment such as BLAST are generally used as they give a reasonable measure for sequence similarity. However, these methods have drawbacks in offering overall sequence similarity, especially in dealing with eukaryotic genomes that often contain many insertions and duplications on sequences. Also these methods do not provide the explicit models for speciation, thus it is difficult to interpret their similarity measure into homology detection. Here, we present a novel method based on Word Conservation Score (WCS) to address the current limitations of homology detection. Instead of counting each amino acid, we adopted the concept of 'Word' to compare sequences. WCS measures overall sequence similarity by comparing word contents, which is much faster than BLAST comparisons. Furthermore, evolutionary distance between homologous sequences could be measured by WCS. Therefore, we expect that sequence comparison with WCS is useful for the multiple-species-comparisons of large genomes. In the performance comparisons on protein structural classifications, our method showed a considerable improvement over BLAST. Our method found bigger micro-syntenic blocks which consist of orthologs with conserved gene order. By testing on various datasets, we showed that WCS gives faster and better overall similarity measure compared to BLAST.

• Bulletin of the Korean Mathematical Society
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• v.36 no.4
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• pp.747-754
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• 1999

We compute the mod p homology of the double loop space of Sp(n)/U(n) by the Serre spectral sequence and the Eilenberg-Moore spectral sequence with the homology operations.

• Bulletin of the Korean Mathematical Society
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• v.40 no.2
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• pp.281-288
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• 2003

We compute the mod p homology of the double loop space of 50(2n)/U(n) by the Serre spectral sequence of Hopf algebras. We also obtain the torsion information of the integral homology.

• Journal of the Korean Society for Industrial and Applied Mathematics
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• v.25 no.4
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• pp.296-311
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• 2021

Topological Data Analysis (TDA), a relatively new field of data analysis, has proved very useful in a variety of applications. The main persistence tool from TDA is persistent homology in which data structure is examined at many scales. Representations of persistent homology include persistence barcodes and persistence diagrams, both of which are not straightforward to reconcile with traditional machine learning algorithms as they are sets of intervals or multisets. The problem of faithfully representing barcodes and persistent diagrams has been pursued along two main avenues: kernel methods and vectorizations. One vectorization is the Betti sequence, or Betti curve, derived from the persistence barcode. While the Betti sequence has been used in classification problems in various applications, to our knowledge, the stability of the sequence has never before been discussed. In this paper we show that the Betti sequence is unstable under the 1-Wasserstein metric with regards to small perturbations in the barcode from which it is calculated. In addition, we propose a novel stabilized version of the Betti sequence based on the Gaussian smoothing seen in the Stable Persistence Bag of Words for persistent homology. We then introduce the normalized cumulative Betti sequence and provide numerical examples that support the main statement of the paper.

• Korean Journal of Microbiology
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• v.26 no.3
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• pp.155-161
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• 1988

Nucleotide sequence homology between bovine, simian, and porcine rotavirus was determined by the RNA:RNA hybridization technique. Single stranded RNA, prepared in vitro with EDTA activated endogeneous viral RNA polymerase, was hhbridized with tritium labeled bovine rotavirus genomic RNA. The heteroduplex RNA was treated with single stranded RNA specific ribonucleases and the RNase resistant hybrid RNA was precipitated, and collected by filtration on a filter paper. Seventy four percent RNA sequence homology between bovine and simian rotavirus and 8 percent RNA sequence homology between bovine and porcine rotavirus was confirmed by hybridization between tritium labeled single stranded RNA and viral genomic RNA.

• Journal of the Korean Mathematical Society
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• v.45 no.3
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• pp.699-709
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• 2008

We study homology of the gauge group associated with the principal $G_2$ bundle over the four-sphere using the Eilenberg-Moore spectral sequence and the Serre spectral sequence with the aid of homology and cohomology operations.

• The Korean Journal of Mycology
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• v.28 no.1
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• pp.22-25
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• 2000

This study was carried out to compare DNA sequence of mating type locus concerning with direct formation of fruiting body in Schizophyllum commune which is growing in North America with that of same species growing in South America. The nucleotide sequence appeared to have about 96% homology to 1-71 $A{\alpha}3$ allele from South America strain, showing a conservative feature. The polypeptide sequence showed about 82% homology when compared partially with mating activity region of 1-71 $A{\alpha}3$ allele. In addition, this polypeptide sequence indicated 74% and 82% identity in homeodomain and acidic-rich regions known as a transcription factor respectively.

• Bulletin of the Korean Mathematical Society
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• v.43 no.1
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• pp.63-75
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• 2006

We study the homology of based gauge groups associated with the principal Spin(n) bundles over the four-sphere using the Eilenberg-Moore spectral sequence and the Serre spectral sequence with the Dyer-Lash of operations.

• Journal of Microbiology
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• v.33 no.3
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• pp.260-266
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• 1995

Hepatitis C virus (HCV) has been considered as a mojor causative agent of post-transfusion related non-A, non-B hepatitis. In this study, the cDNA sequence of NS4 region of HCV (HCV-S) obtained from a Korean patient's plasms was determined. Comparative nucleotide sequence analysis between to type II. 67.2% homology to type III, and 66.4% homology to type IV. The putative amino acid sequence homologies to types I, II, III, and IV were 82.8-84.7%, 92.5-95.1%. 72.5, and 71.1%, respectively. This data strongly suggests that HCV-S should be classified as type II. Significant similarities of hydrophobicity profiles and putative transmembranous domains were found in HCV-S and four major prototypes, indicating that the protein structure is similar in spite of the heterogeneities of intertype homologies at the level of the psrimary nucleotide and amino acid sequences.