• Genomics & Informatics
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• v.16 no.3
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• pp.65-70
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• 2018

The non-coding DNA in eukaryotic genomes encodes a language which programs chromatin accessibility, transcription factor binding, and various other activities. The objective of this short report was to determine the impact of primary DNA sequence on the epigenomic landscape across 200-base pair genomic units by integrating nine publicly available ChromHMM Browser Extensible Data files of the Encyclopedia of DNA Elements (ENCODE) project. The nucleotide frequency profiles of nine chromatin annotations with the units of 200 bp were analyzed and integrative Markov chains were built to detect the Markov properties of the DNA sequences in some of the active chromatin states of different ChromHMM regions. Our aim was to identify the possible relationship between DNA sequences and the newly built chromatin states based on the integrated ChromHMM datasets of different cells and tissue types.

• Journal of Microbiology and Biotechnology
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• v.4 no.4
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• pp.274-277
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• 1994

We subcloned two chicken H3 histone genes and transfected them into Rat 3 cell line. One contains 300 bp 5' to its cap site and the other contains 130 bp 5' to its cap site when cloned into plasm ids. Both of them showed 5' phase specific expression of their mRNA about 8 fold higher (during 5' phase) than during Gl phase. This means that only 130 bp 5' to its cap site was enough to confer cell cycle regulated expression of the latter gene. The DNA sequences of their 5' flanking region did not reveal any particular homologies or subtype-specific sequences. The DNA sequence data also showed that even though the protein coding regions of the histone genes have been conserved exceptionally well throughout evolution, their 5' untranslated regions have not been conserved as well.

• The Journal of Korean Institute of Communications and Information Sciences
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• v.21 no.1
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• pp.1-16
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• 1996

In this paper, by combining the motion compensated transform coding with the sub-band decomposition technique, we present a motion compensated sub-band coding technique(MCSBC) for image sequence coding. Several problems related to the MCSBC, such as a scheme for motion compensation in each sub-band and the efficient VWL coding of the DCT coefficients in each sub-band are discussed. For an efficient coding, the motion estimation and compensation is performed only on the LL sub-band, but the discrete cosine transform(DCT) is employed to encode all sub-bands in our approach. Then, the transform coefficients in each sub-band are scanned in a different manner depending on the energy distributions in the DCT domain, and coded by using separate 2-D Huffman code tables, which are optimized to the probability distributions in the DCT domain, and coded by using separate 2-D Huffman code tables, which are optimized to the probability distribution of each sub-band. The performance of the proposed MCSBC technique is intensively examined by computer simulations on the HDTV image sequences. The simulation results reveal that the proposed MCSBC technique outperforms other coding techniques, especially the well-known motion compensated transform coding technique by about 1.5dB, in terms of the average peak signal to noise ratio.

• Journal of Broadcast Engineering
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• v.10 no.3
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• pp.340-347
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• 2005

This paper presents a polyphase down sampling based multiple description coding applied to H.264 video coding standard. For a given macroblock, a residual macroblock is calculated by motion estimation, and before applying DCT, quantization and entrophy coding of the H.264 coding process, the polyphase down sampling is applied to the residual macroblock to code in four separate descriptions. Experiments were performed for all the 9 test sequences of JVT SVC standardization in various packet loss patterns. Experimental results show that the proposed one gives 0.5 to 5 dB enhancement over an error-concealment based on the slice group map technolgoy.

• Journal of Microbiology and Biotechnology
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• v.5 no.3
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• pp.125-131
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• 1995

A 3, 346 bp of the cdd upstream region in Bacillus subtilis was sequenced from the pSO1 (Song BH and J Neuhard. 1989. Mol. Gen. Genet 216: 462-468) and sequence homology was searched to the known genes in Genbank and European Molecular Biology Laboratory databanks. Five complete and one truncated putative coding sequences deduced from the nucleotide sequence were found through the ORF searching by Genetyx and Macvector software, and one of them was identified as the dgk (diacylglycerol kinase) gene and another, a truncated one, as the phoH (phosphate starvation-inducible gene) gene. The B. subtilis dgk gene, having a role for response to several environmental stress signals, revealed an open reading frame of 134 amino acids with 43.1% of sequence identity to the Streptococcus mutans dgk gene. The carboxy terminal 59 residues of the truncated phoH gene showed 52.7% and 34.5% of sequence identity in amino acids with the corresponding genes of Mycobacterium leprae and Escherichia coli. The four remaining coding sequences consisting of 115, 421, 91, and 91 residues were thought to be unknown ORFs because they have no significant similarity to known genes.

• The KIPS Transactions:PartC
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• v.13C no.1 s.104
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• pp.75-82
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• 2006

In this paper, a space-frequency coded orthogonal frequency division multiplexing (SFC-OFDM) scheme with dual Viterbi decoder is proposed and analyzed. Here, two independent half-rate OFDM symbols are generated after convolutional coding of the binary source code. A dual Viterbi decoder is exploited to decode the demodulated sequences independently in the receiver, and their path metrics are compared. Accordingly, the recovered binary data in the proposed scheme are composed of the combination of the sequences having larger path metrics while those in a conventional system are simply the output of single Viterbi decoder. As a result, the proposed SFC-OFDM scheme has a better performance than the conventional one for all signal-to-noise power ratio.

• Genomics & Informatics
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• v.20 no.4
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• pp.43.1-43.18
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• 2022

Atropa belladonna is a valuable medicinal plant and a commercial source of tropane alkaloids, which are frequently utilized in therapeutic practice. In this study, bioinformatic methodologies were used to examine the pattern of coding sequences and the factors that might influence codon usage bias in the chloroplast genome of Atropa belladonna and other nightshade genomes. The chloroplast engineering being a promising field in modern biotechnology, the characterization of chloroplast genome is very important. The results revealed that the chloroplast genomes of Nicotiana tabacum, Solanum lycopersicum, Capsicum frutescens, Datura stramonium, Lyciumbarbarum, Solanum melongena, and Solanum tuberosum exhibited comparable codon usage patterns. In these chloroplast genomes, we observed a weak codon usage bias. According to the correspondence analysis, the genesis of the codon use bias in these chloroplast genes might be explained by natural selection, directed mutational pressure, and other factors. GC12 and GC3S were shown to have no meaningful relationship. Further research revealed that natural selection primarily shaped the codon usage in A. belladonna and other nightshade genomes for translational efficiency. The sequencing properties of these chloroplast genomes were also investigated by investing the occurrences of palindromes and inverted repeats, which would be useful for future research on medicinal plants.

• Microbiology and Biotechnology Letters
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• v.25 no.1
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• pp.23-29
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• 1997

The nucleotide sequence of the estI gene encoding acetylxylan esterase I of Bacillus stearothermophilus was determined and analyzed. The estI gene was found to consist of a 810 base pair open reading frame coding for a polypeptide of 270 amino acids with a deduced molecular weight of 30 kDa. This was in well agreement with the molecular weight (29 kDa) estimated by SDS-PAGE of the purified esterase. The coding sequence was preceded by a putative ribo some binding site 10 bp upsteam of the ATG codon. Further 53 bp upstream, the transcription initiation signals were identified. The putative $_{-}$10 sequence (TCCAAT) and $_{-}$35 seqence (TTGAAT) corresponded closely to the respective consensus sequences for the Bacillus subtiis major RNA polymerase. The G+C content of the coding region of the estI was 51% whereas that of the third position of codone was 60.2%. The N-terminal amino acid sequence of the EstI deduced from the nucleotide sequence perfectly matched the corresponding region of the purified esterase described previously. Comparison with the amino acid sequence of other esterases and lipases reported so far allowed us to identify a sequence, GLSMG at positions 123 to 127 of the EstI which was reported to be the highly conserved active site sequence for those enzymes. The nucleotide sequence of the estI revealed 55.7% homology to that of the xylC coding for the acetylxylan esterase of Caldocellum saccharolyticum.

• The Journal of Korean Institute of Communications and Information Sciences
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• v.32 no.6C
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• pp.579-584
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• 2007

Recently various prediction structures have been proposed to exploit inter-view correlation among multi-view video sequences. In this paper, we propose a QP(quantization parameter) selection method for the B frame inserted in the first frames of each GOP(group of pictures), where we change QP for the B frame adaptively to achieve uniform picture quality and overall coding gain. Each B frame is coded with reference to two frames in its adjacent views. We calculate QP for the B frame based on the correlation between the two reference frames, calculated using their rate-distortion costs. By applying the proposed method to the MVC reference prediction structure, we have improved the coding gain by 0.09$\sim$0.16 dB.

• KSII Transactions on Internet and Information Systems (TIIS)
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• v.11 no.3
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• pp.1684-1699
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• 2017

The deblocking filter (DF) reduces blocking artifacts in encoded video sequences, and thereby significantly improves the subjective and objective quality of videos. Statistics show that the DF accounts for 5-18% of the total decoding time in high-efficiency video coding. Therefore, speeding up the DF will improve codec performance, especially for the decoder. In view of the rapid development of multicore technology, we propose a parallel DF scheme based on a modified order of accessing the coding tree units (CTUs) by analyzing the data dependencies between adjacent CTUs. This enables the DF to run in parallel, providing accelerated performance and more flexibility in the degree of parallelism, as well as finer parallel granularity. We additionally solve the problems of variable privatization and thread synchronization in the parallelization of the DF. Finally, the DF module is parallelized based on the HM16.1 reference software using OpenMP technology. The acceleration performance is experimentally tested under various numbers of cores, and the results show that the proposed scheme is very effective at speeding up the DF.