Sorting permutations by cut-circularize-linearize-and-paste operations

<p>Abstract</p> <p>Background</p> <p>Genome rearrangements are studied on the basis of genome-wide analysis of gene orders and important in the evolution of species. In the last two decades, a variety of rearrangement operations, such as reversals, transpositions, block-interchanges, translocations, fusions and fissions, have been proposed to evaluate the differences between gene orders in two or more genomes. Usually, the computational studies of genome rearrangements are formulated as problems of sorting permutations by rearrangement operations.</p> <p>Result</p> <p>In this article, we study a sorting problem by cut-circularize-linearize-and-paste (CCLP) operations, which aims to find a minimum number of CCLP operations to sort a signed permutation representing a chromosome. The CCLP is a genome rearrangement operation that cuts a segment out of a chromosome, circularizes the segment into a temporary circle, linearizes the temporary circle as a linear segment, and possibly inverts the linearized segment and pastes it into the remaining chromosome. The CCLP operation can model many well-known rearrangements, such as reversals, transpositions and block-interchanges, and others not reported in the biological literature. In addition, it really occurs in the immune response of higher animals. To distinguish those CCLP operations from the reversal, we call them as non-reversal CCLP operations. In this study, we use permutation groups in algebra to design an <it>O</it>(<it>δn</it>) time algorithm for solving the weighted sorting problem by CCLP operations when the weight ratio between reversals and non-reversal CCLP operations is 1:2, where <it>n</it> is the number of genes in the given chromosome and <it>δ</it> is the number of needed CCLP operations.</p> <p>Conclusion</p> <p>The algorithm we propose in this study is very simple so that it can be easily implemented with 1-dimensional arrays and useful in the studies of phylogenetic tree reconstruction and human immune response to tumors.</p

Scaffolding Contigs Using Multiple Reference Genomes

Scaffolding is an important step of the genome assembly and its function is to order and orient the contigs in the assembly of a draft genome into larger scaffolds. Several single reference-based scaffolders have currently been proposed. However, a single reference genome may not be sufficient alone for a scaffolder to correctly scaffold a target draft genome, especially when the target genome and the reference genome have distant evolutionary relationship or some rearrangements. This motivates researchers to develop the so-called multiple reference-based scaffolders that can utilize multiple reference genomes, which may provide different but complementary types of scaffolding information, to scaffold the target draft genome. In this chapter, we will review some of the state-of-the-art multiple reference-based scaffolders, such as Ragout, MeDuSa and Multi-CAR, and give a complete introduction to Multi-CSAR, an improved extension of Multi-CAR

iPARTS: an improved tool of pairwise alignment of RNA tertiary structures

iPARTS is an improved web server for aligning two RNA 3D structures based on a structural alphabet (SA)-based approach. In particular, we first derive a Ramachandran-like diagram of RNAs by plotting nucleotides on a 2D axis using their two pseudo-torsion angles η and θ. Next, we apply the affinity propagation clustering algorithm to this η-θ plot to obtain an SA of 23-nt conformations. We finally use this SA to transform RNA 3D structures into 1D sequences of SA letters and continue to utilize classical sequence alignment methods to compare these 1D SA-encoded sequences and determine their structural similarities. iPARTS takes as input two RNA 3D structures in the PDB format and outputs their global alignment (for determining overall structural similarity), semiglobal alignments (for detecting structural motifs or substructures), local alignments (for finding locally similar substructures) and normalized local structural alignments (for identifying more similar local substructures without non-similar internal fragments), with graphical display that allows the user to visually view, rotate and enlarge the superposition of aligned RNA 3D structures. iPARTS is now available online at http://bioalgorithm.life.nctu.edu.tw/iPARTS/

A Real World Report on Intravenous High-Dose and Non-High-Dose Proton-Pump Inhibitors Therapy in Patients with Endoscopically Treated High-Risk Peptic Ulcer Bleeding

Background and Study Aims. The optimal dose of intravenous proton-pump inhibitor (PPI) therapy for the prevention of peptic ulcer (PU) rebleeding remains controversial. This study aimed to understand the real world experiences in prescribing high-dose PPI and non-high-dose PPI for preventing rebleeding after endoscopic treatment of high-risk PU. Patients and Methods. A total of 220 subjects who received high-dose and non-high-dose pantoprazole for confirmed acute PU bleeding that were successfully treated endoscopically were enrolled. They were divided into rebleeding (n = 177) and non-rebleeding groups (n = 43). Randomized matching of the treatment-control group was performed. Patients were randomly selected for non-high-dose and high-dose PPI groups (n = 44 in each group). Results. Univariate analysis showed, significant variables related to rebleeding were female, higher creatinine levels, and higher Rockall scores ( 6). Before case-control matching, the high-dose PPI group had higher creatinine level, higher percentage of shock at presentation, and higher Rockall scores. After randomized treatment-control matching, no statistical differences were observed for rebleeding rates between the high-dose and non-high-dose groups after casecontrol matching. Conclusion. This study suggests that intravenous high-dose pantoprazole may not be superior to non-high-dose regimen in reducing rebleeding in high-risk peptic ulcer bleeding after successful endoscopic therapy

Gene-Gene Interactions in Renin-Angiotensin-Aldosterone System Contributes to End-Stage Renal Disease Susceptibility in a Han Chinese Population

Objective. In this study, we investigated whether RAAS gene single nucleotide polymorphisms (SNPs) and their interactions were associated with end-stage renal stage (ESRD). Methodology and Results. This was a case-control study for 647 ESRD cases and 644 controls. AGT (M235T (rs699) and T174M (rs4762)), AGTR1 (A1166C (rs5186) and C573T (rs5182)), ACE (I/D (rs1799752) and G2350A (rs4343)), and CYP11B2 C-344T (rs1799998) were genotyped and compared between cases and controls to identify SNPs associated with ESRD susceptibility. Multifactor dimensionality reduction (MDR) was used to identify gene-gene interactions. Several RAAS genes were associated with ESRD: AGT M235T, ACE I/D, ACE G2350A, and CYP11B2 C-344T. By MDR analysis, a three-locus model (ACE ID/ACE G2350A/CYP11B2 C-344T) of gene-gene interaction was the best for predicting ESRD risk, and its maximum testing accuracy was 56.08% and maximum cross-validation consistency was 9/10. ESRD risk was higher with the simultaneous occurrence of ACE I/D DD-ACE G2350A AA. AGT, ACE, and CYP11B2 gene polymorphisms are associated with ESRD. Conclusions. The gene-gene interaction effects of ACE I/D, ACE G2350A, and CYP11B2 C-344T polymorphisms are more important than individual factors for ESRD development among Han Chinese