• Genomics & Informatics
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• v.4 no.4
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• pp.167-169
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• 2006

PABAP (Palindrome Analysis by BLAST Program) is an analysis system that identifies palindromic sequences from a large genome sequence up to several megabases long. It uses NCBI BLAST as a searching engine, and data processing such as alignment filtration and detection of inverted repeats which satisfy user-defined parameters is performed by manipulating data after populating into a MySQL database. PABAP outperforms publicly available palindrome search program in that it can detect large palindrome with internal spacer at a faster speed from bacterial genomes. It is a standalone application and is freely available for noncommercial users.

• Journal of the Korean Mathematical Society
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• v.52 no.4
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• pp.765-780
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• 2015

We consider the problem of characterizing the palindromic sequences ${\langle}c_{d-1},\;c_{d-2}\;,{\cdots},\;c_0\rangle$, $c_{d-1}{\neq}0$, having the property that for any $K{\in}\mathbb{N}$ there exists a number that is a palindrome simultaneously in K different bases, with ${\langle}c_{d-1},\;c_{d-2}\;,{\cdots},\;c_0\rangle$ being its digit sequence in one of those bases. Since each number is trivially a palindrome in all bases greater than itself, we impose the restriction that only palindromes with at least two digits are taken into account. We further consider a related problem, where we count only palindromes with a fixed number of digits (that is, d). The first problem turns out not to be very hard; we show that all the palindromic sequences have the required property, even with the additional point that we can actually restrict the counted palindromes to have at least d digits. The second one is quite tougher; we show that all the palindromic sequences of length d = 3 have the required property (and the same holds for d = 2, based on some earlier results), while for larger values of d we present some arguments showing that this tendency is quite likely to change.

• Korean Journal of Plant Tissue Culture
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• v.22 no.4
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• pp.201-205
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• 1995

The synthetic oligomers called nos right palindrome (RP) element and left palindrome (LP) element were inserted into nos.minimal promoter nos 5'-101 deletion mutant The activity of nos promoter was measured by studying the expression pattern of gene fusion between nos promoter and reporter genes such as chloramphenicol acetyltransferase and $\beta$-glucuconidase. Analysis of transgenic tobacco plane carrying transgene showed that the activity of nos minimal promoter activity was recovered by insertion of synthetic nos RP element. Nos RP element insertion of nos minimal promoter was induced by auxin, dithiothreitol, salicylic acid and methyl jasmonate.

• The Journal of the Convergence on Culture Technology
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• v.7 no.1
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• pp.145-150
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• 2021

This thesis attempted to examine the mechanization of humans, humanization of machines, and coexistence through dance works. The dance works were reviewed by partial excerpts from Oscar Schlemer's <3 Chord Ballet>, Felindrome Dance Company's , and . Also, I looked at the dance work , which has an inherent form of coexistence. Through the above work, robot-like science and technology and fusion. It was found that various dance performances that coexist in complex forms provide continuous creativity to humans, and various forms of sensibility and creative movements based on data make it possible to produce rich performances for humans. This researcher expects numerous works that accept and reflect the changes of the times through the embodied interaction of dance performances with science and technology.

• Korean Journal of Microbiology
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• v.32 no.3
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• pp.186-191
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• 1994

The origin of the leading strand replication (ori) and of lagging strand replication (M-O) of R-plasmid pSBK203 was identified and its base sequence was determined. About 50 bp of ori sequence residues overlapped with the structural gene of rep. Sequence comparison reveals that pSBK-ori shares obvious identities with those of pT181 family and consists of two regions, one is conserved and the other is variable region. Of two palindrome sequence located one after another in upstream region of rep gene, palA' instead of palA which shares sequence homology with diverse family of plasmids such as pOX6, pC194, and pE194 seems to act as a signal for conversion of primarily replicated ssDNA to dsDNA (minus origin (M-O)).

• Journal of Microbiology and Biotechnology
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• v.5 no.3
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• pp.117-124
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• 1995

A gene (xynA) encoding the endo-xylanase (E.C.3.2.1.8) from Bacillus stearothermophilus was cloned in E. coli, and its complete nucleotide sequence was determined. The xynA gene consists of a 636 base pairs open reading frame coding for a protein of 212 amino acids with a deduced molecular weight of 23, 283 Da. A putative signal sequence of 27 amino acid residues shows the features comparable with the Bacillus signal sequences; namely, the signal contains a positively charged region close to the N-terminus followed by a long hydrophobic string. The coding sequence is preceded by a possible ribosome binding site with a free energy value of -16.6 kcal/mol and the transcription initiation signals are located further upstream. The translation termination codon (TAA) at the 3 end of the coding sequence is followed by two palindrome sequences, one of which is thought to act as a terminator. The xynA gene has a high GC content, especially in the wobble position of codons (64%). Comparison of the primary protein sequence with those of other xylanases shows a high homology to the xylanases belonging to family G.

• The KIPS Transactions:PartB
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• v.14B no.6
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• pp.461-472
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• 2007

The emphasis in genome projects has Been moving towards the sequence analysis in order to extract biological "meaning"(e.g., evolutionary history of particular molecules or their functions) from the sequence. Especially. palindromic or direct repeats that appear in a sequence have a biophysical meaning and the problem is to recognize interesting patterns and configurations of words(strings of characters) over complementary alphabets. In this paper, we propose an algorithm to identify variable length palindromic pairs(longer than a threshold), where we can allow gaps(distance between words). The algorithm is called palindrome algorithm(PA) and has O(N) time complexity. A palindromic pair consists of a hairpin structure. By composing collected palindromic pairs we build n-pair palindromic patterns. In addition, we dot some of the longest pairs in a circle to represent the structure of a DNA sequence. We run the algorithm over several selected genomes and the results of E.coli K12 are presented. There existed very long palindromic pair patterns in the genomes, which hardly occur in a random sequence.

• Kyungpook Mathematical Journal
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• v.56 no.2
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• pp.349-355
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• 2016

For any integer $n{\geq}2$, each palindrome of n induces a circulant graph of order n. It is known that for each integer $n{\geq}2$, there is a one-to-one correspondence between the set of (resp. aperiodic) palindromes of n and the set of (resp. connected) circulant graphs of order n (cf. [2]). This bijection gives a one-to-one correspondence of the palindromes ${\sigma}$ with $gcd({\sigma})=1$ to the connected circulant graphs. It was also shown that the number of palindromes ${\sigma}$ of n with $gcd({\sigma})=1$ is the same number of aperiodic palindromes of n. Let $a_n$ (resp. $b_n$) be the number of aperiodic palindromes ${\sigma}$ of n with $gcd({\sigma})=1$ (resp. $gcd({\sigma}){\neq}1$). Let $c_n$ (resp. $d_n$) be the number of periodic palindromes ${\sigma}$ of n with $gcd({\sigma})=1$ (resp. $gcd({\sigma}){\neq}1$). In this paper, we calculate the numbers $a_n$, $b_n$, $c_n$, $d_n$ in two ways. In Theorem 2.3, we $n_d$ recurrence relations for $a_n$, $b_n$, $c_n$, $d_n$ in terms of $a_d$ for $d{\mid}n$ and $d{\neq}n$. Afterwards, we nd formulae for $a_n$, $b_n$, $c_n$, $d_n$ explicitly in Theorem 2.5.