Multiple alignment

Ebook "Introduction to computational biology: An evolutionary approach" Analysis of molecular sequence data is the main subject of this introduction to computational biology. There are two closely connected aspects to biological sequences: (i) their relative position in the space of all other sequences, and (ii) their movement through this sequence space in evolutionary time. Accordingly, the first part of the book deals with classical methods of sequence analysis: pairwise alignment, exact string matching, multiple alignment, and hidden Markov models.

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In this study we generated a whole exome sequencing benchmark dataset using the platinum genome sample NA12878 and developed an intersect-then-combine (ITC) approach to increase the accuracy in calling single nucleotide variants (SNVs) and indels in tumour-normal pairs. We evaluated the effect of alignment, base quality recalibration, mutation caller and filtering on sensitivity and false positive rate.

11p vioraclene 31-03-2024 4 2   Download

Expansions of short tandem repeats are the cause of many neurogenetic disorders including familial amyotrophic lateral sclerosis, Huntington disease, and many others. Multiple methods have been recently developed that can identify repeat expansions in whole genome or exome sequencing data.

10p viellison 28-03-2024 3 1   Download

Part 1 of ebook "Strategic project management made simple: Practical tools for leaders and teams" provides readers with contents including: thinking outside the bar chart; mastering strategic project management; building strong project backbones; organizing multiple objectives into trees; introducing the logical framework; aligning projects with strategic intent;...

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Powerful Vocabulary for Reading Success is the first vocabulary program to offer you a systematic, teacher-directed approach to improving your students’ reading achievement. This unique program is: Research-Based. Developed based on research that is proven effective for all students. Aligns to State Standards and No Child Left Behind for Vocabulary Development. Explicit and Comprehensive. An easy-to-manage, complete instructional program that models effective word learning and gives multiple exposures to hundreds of important words to ensure mastery.

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Powerful Vocabulary for Reading Success is the first vocabulary program to offer you a systematic, teacher-directed approach to improving your students’ reading achievement. This book gives instruction for hundreds of high-utility, academic and content-area words and effective tools for deciphering hundreds more unknown words all found on state and national tests. A powerful combination for ensuring higher test scores. Powerful Vocabulary for Reading Success is the first vocabulary program to offer you a systematic, teacher-directed approach to improving your students’ reading achievement.

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In this paper, we describe our approach to tackle this problem: we first preprocess the training data then use it to train a FastSpeech2 acoustic model with some replacements in the external aligner model, finally we use HiFiGAN vocoder to construct the waveform.

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This study aims to identify the multiple intelligence (MI) profiles of EFL students at a Vietnamese university with Gardner’s Multiple Intelligence Theory. It also analyzed MIs manifested in activities in Life textbook being used in English courses for university students to determine how well they align with the students’ profiles.

15p vighostrider 01-06-2023 10 4   Download

Single cell experimental techniques reveal transcriptomic and epigenetic heterogeneity among cells, but how these are related is unclear. We present MATCHER, an approach for integrating multiple types of single cell measurements. MATCHER uses manifold alignment to infer single cell multi-omic profiles from transcriptomic and epigenetic measurements performed on different cells of the same type.

19p vialfrednobel 29-01-2022 7 1   Download

Distinguishing biological from technical variation is crucial when integrating and comparing single-cell genomics datasets across different experiments. Existing methods lack the capability in explicitly distinguishing these two variations, often leading to the removal of both variations.

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The cDNA encoding lipase enzyme was cloned from Olea europaea var. europaea cv. Gemlik leaves using the RACE method. The full nucleotide sequence was 1546 bp long and encoded a putative protein of 412 amino acid long protein. The amino acid sequence showed identity to Triacylglycerol Lipase 1 sequences from different plants. A phylogenetic tree was constructed showing relations with various plant lipases.

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The increasing application of next generation sequencing technologies has led to the availability of thousands of reference genomes, often providing multiple genomes for the same or closely related species. The current approach to represent a species or a population with a single reference sequence and a set of variations cannot represent their full diversity and introduces bias towards the chosen reference.

12p vilarryellison 29-10-2021 20 1   Download

Several methods have been developed for the accurate reconstruction of gene trees. Some of them use reconciliation with a species tree to correct, a posteriori, errors in gene trees inferred from multiple sequence alignments. Unfortunately the best fit to sequence information can be lost during this process.

11p vibeauty 23-10-2021 14 1   Download

Proteins play essential roles in almost all life processes. The prediction of protein function is of significance for the understanding of molecular function and evolution. Network alignment provides a fast and effective framework to automatically identify functionally conserved proteins in a systematic way.

7p vijeeni2711 24-07-2021 11 0   Download

Walnut (Juglans regia) is an important tree cultivated worldwide and is exposed to a series of both abiotic and biotic stress during their life-cycles. The heat stress transcription factors (HSFs) play a crucial role in plant response to various stresses by regulating the expression of stress-responsive genes.

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The study found, among other things, that incorporating existing policies into the multiple ministries and affiliated institutions together with the current industry-led policy initiatives to manage ESG risks are not adequate. Hence it is recommended various insights to be taken into consideration by the policymakers to formulate a national framework for mobilizing public and private capital to meet the goals of sustainability

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We analyze phylogenetic tree building methods from molecular sequences (PTMS). These are methods which base their construction solely on sequences, coding DNA or amino acids.

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The distance matrix computed from multiple alignments of homologous sequences is widely used by distance-based phylogenetic methods to provide information on the evolution of protein families. This matrix can also be visualized in a low dimensional space by metric multidimensional scaling (MDS).

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Aligning short DNA reads to a reference sequence alignment is a prerequisite for detecting their biological origin and analyzing them in a phylogenetic context. With the PaPaRa tool we introduced a dedicated dynamic programming algorithm for simultaneously aligning short reads to reference alignments and corresponding evolutionary reference trees.

12p viwyoming2711 16-12-2020 10 1   Download

The detection of significant compensatory mutation signals in multiple sequence alignments (MSAs) is often complicated by noise. A challenging problem in bioinformatics is remains the separation of significant signals between two or more non-conserved residue sites from the phylogenetic noise and unrelated pair signals.

12p viwyoming2711 16-12-2020 12 1   Download