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**11 - 16**of**16**### unknown title

, 2005

"... Scoring schemes of palindrome clusters for more sensitive prediction of replication origins in herpesviruses ..."

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Scoring schemes of palindrome clusters for more sensitive prediction of replication origins in herpesviruses

### unknown title

"... The SMAD4 gene codes for cell-signaling proteins that prevent abnormal vascular growths. DNA palindromes are inversely proportional sequences that play roles in gene expression through the formation of stem-loops and disease/tumor detection. Previous research approximated that there were 100 palindr ..."

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The SMAD4 gene codes for cell-signaling proteins that prevent abnormal vascular growths. DNA palindromes are inversely proportional sequences that play roles in gene expression through the formation of stem-loops and disease/tumor detection. Previous research approximated that there were 100 palindromes in every 1000 base pairs of a randomly generated sequence. A Java program was written to mutate fasta sequences based on ARUP’s SMAD4 database, information from NCBI, and random locations and another was written to find palindromes in the DNA sequences and output their lengths. These lengths were plotted sequentially using the Mathematica software. By measuring shifts in each mutated plot superimposed on the wild type plot, the number of pixels shifted between peaks was recorded and, using a scale which was measured to be 12 pixels per 100 palindromes, converted into the number of palindromes deleted. The amount of base pairs (bp) deleted was proportional to the amount of palindromes deleted. The relationship between bp and palindromes is described by the equation p=round(-0.242996+0.425309*l) such that p represents the number of palindromes and l represents the length of a sequence. This linear regression shows that palindromes are evenly distributed throughout the SMAD4 gene assuming the distribution follows a Poisson distribution. Out of every 1000 bp, there are approximately 420 palindromes in the SMAD4 mRNA which is approximately 475 palindromes in SMAD4’s Primary Assembly genomic region. The SMAD4 gene exhibits 275 (137.5%) more palindromes than the randomly generated palindromic distribution projected by previous research. Finding the distribution of palindromes in RNA molecules can lead to future research and classification of key regions that determine the shape of secondary, tertiary, and quaternary structures.

### © Institute of Mathematical Statistics, 2004 STEIN’S METHOD, PALM THEORY AND POISSON

"... The framework of Stein’s method for Poisson process approximation is presented from the point of view of Palm theory, which is used to construct Stein identities and define local dependence. A general result (Theorem 2.3) in Poisson process approximation is proved by taking the local approach. It is ..."

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The framework of Stein’s method for Poisson process approximation is presented from the point of view of Palm theory, which is used to construct Stein identities and define local dependence. A general result (Theorem 2.3) in Poisson process approximation is proved by taking the local approach. It is obtained without reference to any particular metric, thereby allowing wider applicability. A Wasserstein pseudometric is introduced for measuring the accuracy of point process approximation. The pseudometric provides a generalization of many metrics used so far, including the total variation distance for random variables and the Wasserstein metric for processes as in Barbour and Brown [Stochastic Process. Appl. 43 (1992) 9–31]. Also, through the pseudometric, approximation for certain point processes on a given carrier space is carried out by lifting it to one on a larger space, extending an idea of Arratia, Goldstein and Gordon [Statist. Sci. 5 (1990) 403–434]. The error bound in the general result is similar in form to that for Poisson approximation. As it yields the Stein factor 1/λ as in Poisson approximation, it provides good approximation, particularly in cases where λ is large. The general result is applied to a number of problems including Poisson process modeling of rare words in a DNA sequence. 1. Introduction. Poisson

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"... Finding differentially expressed regions of arbitrary length in quantitative genomic data based on marked point process model ..."

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Finding differentially expressed regions of arbitrary length in quantitative genomic data based on marked point process model

### origins

, 2005

"... Scoring schemes of palindrome clusters for more sensitive prediction of replication ..."

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Scoring schemes of palindrome clusters for more sensitive prediction of replication

### IN SCHOOL ARTICLE Discovering the Distribution of Palindromic Sequences in the SMAD4 Gene using Large and Medium Deletions and the Resulting RNA Structure Predictions

"... The SMAD4 gene codes for cell-signaling proteins that prevent abnormal vascular growths. DNA palindromes are inversely proportional sequences that play roles in gene expression through the formation of stem-loops and disease/tumor detection. Previous research approximated that there were 100 palindr ..."

Abstract
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The SMAD4 gene codes for cell-signaling proteins that prevent abnormal vascular growths. DNA palindromes are inversely proportional sequences that play roles in gene expression through the formation of stem-loops and disease/tumor detection. Previous research approximated that there were 100 palindromes in every 1000 base pairs of a randomly generated sequence. A Java program was written to mutate fasta sequences based on ARUP’s SMAD4 database, information from NCBI, and random locations and another was written to find palindromes in the DNA sequences and output their lengths. These lengths were plotted sequentially using the Mathematica software. By measuring shifts in each mutated plot superimposed on the wild type plot, the number of pixels shifted between peaks was recorded and, using a scale which was measured to be 12 pixels per 100 palindromes, converted into the number of palindromes deleted. The amount of base pairs (bp) deleted was proportional to the amount of palindromes deleted. The relationship between bp and palindromes is described by the equation p=round(-0.242996+0.425309*l) such that p represents the number of palindromes and l represents the length of a sequence. This linear regression shows that palindromes are evenly distributed throughout the SMAD4 gene assuming the distribution follows a Poisson distribution. Out of every 1000 bp, there are approximately 420 palindromes in the SMAD4 mRNA which is approximately 475 palindromes in SMAD4’s Primary Assembly genomic region. The SMAD4 gene exhibits 275 (137.5%) more palindromes than the randomly generated palindromic distribution projected by previous research. Finding the distribution of palindromes in RNA molecules can lead to future research and classification of key regions that determine the shape of secondary, tertiary, and quaternary structures.