Sentences with phrase «genome size using»

By developing a computational shortcut to rapidly estimate genome size using statistical modeling, Dr. Pollard's team has been able to improve the accuracy of microbiome studies.

Not exact matches

So for his final - year research project he went to the Institute to study population genetics — in particular, how parameters such as population and genome size may affect the evolution of populations — using computer models.

In existing vertebrates, genome size correlates very closely with bone cell size, so Organ used the size of dinosaur bone cells to predict how much genetic material the extinct animals possessed.

Pairwise alignments were calculated using Shuffle - LAGAN (window size, 400 bp; step size 40 bp; translated anchoring), a glocal alignment algorithm that is able to calculate optimal alignments by using both local alignments and global maps of sequence rearrangements (e.g. duplications of the fiber gene in adenovirus genomes with 2 fibers)[57].

Reads were then aligned using BLASTN (word size = 11, E-value = 1 × 10 − 5) and TBLASTX (word size = 11, E-value = 1 × 10 − 5) to the genome sequence of SAdV - 18 (Fig. 2B).

They used the following equation; (2) where GE is the size of the extant genome, GA is the size of the ancestral genome, GG is the amount of lineage - specific genome gain and GL is the amount of lineage - specific genome loss.

Importantly, our decision to use a synthetic genome meant that placed chain - gaps larger than our window size would spread across window boundaries, ensuring that genomic bins would contain no more than 200 kb of sequence.

Using Eq 2 and solving for GA with extant genome sizes from Table 1 and gain and loss rates calculated by the recent transposon method (Table 2), we get estimated ancestral genome sizes of 2.64 Gb and 2.66 Gb for human and mouse respectively.

The paper maps passenger pigeon genetic data to a published genome from the Rock dove, Columba livia, and uses these data to infer changes in their population size through time.

The DNA has fragmented in an uncontrolled fashion, creating a mix of fragment sizes — genome assemblers must use fragment lengths of specific size ranges.

When microbiomes are studied using metagenomics — sequencing their total DNA — differences in bacterial genome size can bias the estimation of the proportion of each gene in the sample.

The recent trends in population size were gained using complete mitochondrial genome sequences of of 41 passenger pigeons (three of which date to 4,000 years old).

This is a landmark study not only due to the size, but the systematic characterization of each case using whole - genome sequencing (WGS), exome sequencing (WES), and transcriptome sequencing (RNA - seq).

Genetic studies using samples along the distribution range of both subspecies and based on a few dozen nuclear markers have revealed loci of relatively high divergence (0.3 — 1.2 %) between subspecies embedded in a genome otherwise characterized by low levels of differentiation and high levels of bidirectional gene flow [21], [24]--[26], likely facilitated by high effective population sizes, high dispersal, and a relatively short generation time [21], [24]--[26].

Whole - exome sequencing (WES) and whole - genome sequencing (WGS) simulations were used to calculate detection performance across a range of mosaic event sizes, types, clonalities, and sequencing depths.

Raw single reads (and their mate pairs) from deep sequencing libraries corresponding to 3 XMRV - positive samples [VP35, 14,589,296 reads; VP42, 14,573,990 reads; and VP62 (2006), 18,308,352 reads] and 3 XMRV - negative samples [VP10, 5,270,536 reads; VP30, 4,378,204 reads; and VP62 (2012), 3,985,692 reads] were then stripped of adapter and primer sequences and aligned to the CRS mitochondrial genome using BLASTn (word size = 11, E-value = 1 × 10 − 10).

Previously, researchers including UNC's Karen Mohlke, PhD, and Kari North, PhD, used a smaller sample size to find 48 loci in the genome.

Specification points covered are: Paper 2 Topic 1 (4.5 - homeostasis and response) 4.5.1 - Homeostasis (B5.1 lesson) 4.5.3.2 - Control of blood glucose concentration (B5.1 lesson) 4.5.2.1 - Structure and function (B5.2 lesson) Required practical 7 - plan and carry out an investigation into the effect of a factor on human reaction time (B5.2 lesson) 4.5.3.1 - Human endocrine system (B5.6 lesson) 4.5.3.4 - Hormones in human reproduction (B5.10 lesson) 4.5.3.5 - Contraception (B5.11 lesson) 4.5.3.6 - The use of hormones to treat infertility (HT only)(B5.12 lesson) 4.5.3.7 - Negative feedback (HT only)(B5.13 lesson) Paper 2 topic 2 (4.6 - Inheritance, variation and evolution) 4.6.1.1 - sexual and asexual reproduction (B6.1 lesson) 4.6.1.2 - Meiosis (B6.1 lesson) 4.6.1.4 - DNA and the genome (B6.3 lesson) 4.6.1.6 - Genetic inheritance (B6.5 lesson) 4.6.1.7 - Inherited disorders (B6.6 lesson) 4.6.1.8 - Sex determination (B6.5 lesson) 4.6.2.1 - Variation (B6.9 lesson) 4.6.2.2 - Evolution (B6.10 lesson) 4.6.2.3 - Selective breeding (B6.11 lesson) 4.6.2.4 - Genetic engineering (B6.11 lesson) 4.6.3.4 - Evidence for evolution (B6.16 lesson) 4.6.3.5 - Fossils (B6.16 lesson) 4.6.3.6 - Extinction (B6.16 lesson) 4.6.3.7 - Resistant bacteria (B6.17 lesson) 4.6.4.1 - classification of living organisms (B6.18 lesson) Paper 2 topic 3 (4.7 - Ecology 4.7.1.1 - Communities (B7.1 lesson) 4.7.1.2 - Abiotic factors (B7.1 lesson) 4.7.1.3 - Biotic factors (B7.1 lesson) 4.7.1.4 — Adaptations (B7.2 lesson) 4.7.2.1 - Levels of organisation (feeding relationships + predator - prey cycles)(B7.3 lesson) 4.7.2.1 - Levels of organisation (required practical 9 - population sizes)(B7.4 lesson) 4.7.2.2 - How materials are cycled (B7.5 lesson) 4.7.3.1 - Biodiversity (B7.7 lesson) 4.7.3.6 - Maintaining Biodiversity (B7.7 lesson) 4.7.3.2 - Waste management (B7.9 lesson) 4.7.3.3 - Land use (B7.9 lesson) 4.7.3.4 - Deforestation (B7.9 lesson) 4.7.3.5 - Global warming (B7.9 lesson)