Local alignment of generalized k-base encoded DNA sequence

<p>Abstract</p> <p>Background</p> <p>DNA sequence comparison is a well-studied problem, in which two DNA sequences are compared using a weighted edit distance. Recent DNA sequencing technologies however observe an encoded form of the sequence, rather than each DNA base individually. The encoded DNA sequence may contain technical errors, and therefore encoded sequencing errors must be incorporated when comparing an encoded DNA sequence to a reference DNA sequence.</p> <p>Results</p> <p>Although two-base encoding is currently used in practice, many other encoding schemes are possible, whereby two ore more bases are encoded at a time. A generalized <it>k</it>-base encoding scheme is presented, whereby feasible higher order encodings are better able to differentiate errors in the encoded sequence from true DNA sequence variants. A generalized version of the previous two-base encoding DNA sequence comparison algorithm is used to compare a <it>k</it>-base encoded sequence to a DNA reference sequence. Finally, simulations are performed to evaluate the power, the false positive and false negative SNP discovery rates, and the performance time of <it>k</it>-base encoding compared to previous methods as well as to the standard DNA sequence comparison algorithm.</p> <p>Conclusions</p> <p>The novel generalized <it>k</it>-base encoding scheme and resulting local alignment algorithm permits the development of higher fidelity ligation-based next generation sequencing technology. This bioinformatic solution affords greater robustness to errors, as well as lower false SNP discovery rates, only at the cost of computational time.</p

1934: Abilene Christian College Bible Lectures - Full Text

INTRODUCTION The theme for the Lectures for 1934, “The New Testament Church in History,” is a very timely one and follows naturally the theme of the 1933 Lectures, “The Church We Read About in the New Testament.” There is no subject that is so vital in our work as Christians today as a proper understanding of the great spiritual kingdom of our Savior, the church which was built by Jesus Christ. It is a hard lesson to teach because all people are so dull of hearing concerning things spiritual. Just as Nicodemus marveled when the Christ told him of the spiritual kingdom so do people today wonder and marvel when they are told that there is only one great church, the spiritual kingdom of our Lord and Savior Jesus Christ, and that all the saved of earth belong to that church and that belonging to anything else profits little, and is unnecessary. Not only are numbers of denominational churches and people who have no religious affiliation ignorant of the true meaning of the church, but even those who claim to be members of the one body are lacking in understanding concerning the kingdom of Christ. It is therefore the purpose of the Abilene College Lectures last year, this year and next year to arouse a greater interest in the study and the teaching of this very vital matter. In this particular volume much valuable information is brought together on the trials and struggles of the church from its foundations to the present. The speakers have made careful preparation on their subjects and have given lessons that should prove helpful to all who desire to have a better understanding of the church. Our prayer is that these Lectures may be read by many and that they may do much good in the name of the Christ. Jas. F. Cox,President, Abilene Christian College. Nov. 6, 1934

U87MG Decoded: The Genomic Sequence of a Cytogenetically Aberrant Human Cancer Cell Line

U87MG is a commonly studied grade IV glioma cell line that has been analyzed in at least 1,700 publications over four decades. In order to comprehensively characterize the genome of this cell line and to serve as a model of broad cancer genome sequencing, we have generated greater than 30× genomic sequence coverage using a novel 50-base mate paired strategy with a 1.4kb mean insert library. A total of 1,014,984,286 mate-end and 120,691,623 single-end two-base encoded reads were generated from five slides. All data were aligned using a custom designed tool called BFAST, allowing optimal color space read alignment and accurate identification of DNA variants. The aligned sequence reads and mate-pair information identified 35 interchromosomal translocation events, 1,315 structural variations (>100 bp), 191,743 small (<21 bp) insertions and deletions (indels), and 2,384,470 single nucleotide variations (SNVs). Among these observations, the known homozygous mutation in PTEN was robustly identified, and genes involved in cell adhesion were overrepresented in the mutated gene list. Data were compared to 219,187 heterozygous single nucleotide polymorphisms assayed by Illumina 1M Duo genotyping array to assess accuracy: 93.83% of all SNPs were reliably detected at filtering thresholds that yield greater than 99.99% sequence accuracy. Protein coding sequences were disrupted predominantly in this cancer cell line due to small indels, large deletions, and translocations. In total, 512 genes were homozygously mutated, including 154 by SNVs, 178 by small indels, 145 by large microdeletions, and 35 by interchromosomal translocations to reveal a highly mutated cell line genome. Of the small homozygously mutated variants, 8 SNVs and 99 indels were novel events not present in dbSNP. These data demonstrate that routine generation of broad cancer genome sequence is possible outside of genome centers. The sequence analysis of U87MG provides an unparalleled level of mutational resolution compared to any cell line to date

CENGO: a web-based serious game to increase the programming knowledge levels of computer engineering students

In recent years, games are used to increase the level of knowledge and experience of individuals working in different domains. Especially in the education field, there are several different serious games to teach the subjects of the lectures or other educational materials to students in an enjoyable way. Hence, this study proposes a quantitative research approach to increase the programming knowledge levels of the first-year undergraduate students at computer engineering departments. For this aim, a responsive web platform was developed to teach the syntax and logic of C programming language by using some game elements. Therefore, the students have a chance to repeat the topics related to C programming language continuously since the platform is always accessible. To figure out the efficiency of the designed environment, 10 first-year computer engineering students were selected. According to the results obtained from the user tests, this game can be used as an educational tool, which supports the traditional training methods, to increase the knowledge levels of students about the syntax and logic of C programming language

Theory and applications of atomic and ionic polarizabilities

Atomic polarization phenomena impinge upon a number of areas and processes in physics. The dielectric constant and refractive index of any gas are examples of macroscopic properties that are largely determined by the dipole polarizability. When it comes to microscopic phenomena, the existence of alkaline-earth anions and the recently discovered ability of positrons to bind to many atoms are predominantly due to the polarization interaction. An imperfect knowledge of atomic polarizabilities is presently looming as the largest source of uncertainty in the new generation of optical frequency standards. Accurate polarizabilities for the group I and II atoms and ions of the periodic table have recently become available by a variety of techniques. These include refined many-body perturbation theory and coupled-cluster calculations sometimes combined with precise experimental data for selected transitions, microwave spectroscopy of Rydberg atoms and ions, refractive index measurements in microwave cavities, ab initio calculations of atomic structures using explicitly correlated wave functions, interferometry with atom beams, and velocity changes of laser cooled atoms induced by an electric field. This review examines existing theoretical methods of determining atomic and ionic polarizabilities, and discusses their relevance to various applications with particular emphasis on cold-atom physics and the metrology of atomic frequency standards.Comment: Review paper, 44 page