The khmer software package: enabling efficient nucleotide sequence analysis [version 1; referees: 2 approved, 1 approved with reservations]

The khmer package is a freely available software library for working efficiently with fixed length DNA words, or k-mers. khmer provides implementations of a probabilistic k-mer counting data structure, a compressible De Bruijn graph representation, De Bruijn graph partitioning, and digital normalization. khmer is implemented in C++ and Python, and is freely available under the BSD license at https://github.com/dib-lab/khmer/

Complete Structural Model of Escherichia coli RNA Polymerase from a Hybrid Approach

A combination of structural approaches yields a complete atomic model of the highly biochemically characterized Escherichia coli RNA polymerase, enabling fuller exploitation of E. coli as a model for understanding transcription

Association of fitness wellness and work-related low back pain among DLSMHSI BSPT batch 2023 students SY 2021-2022

The study was conducted to determine the “Association of Fitness Wellness and WorkRelated Low Back Pain Among DLSMHSI BSPT Batch 2023 Students S.Y. 2021-2022”. The study utilized a descriptive correlational approach that focuses on quantitative data analysis. A total of 68 responses were gathered using a non-probability sampling approach known as quota sampling, with 23 respondents being eliminated during the pre-screening process, leaving 45 participants in the study. A self-made questionnaire that was transferred to Google forms was used to collect quantitative data from the respondents. The findings revealed that 12 out of 30 had an interpretation of average fitness wellness level; 5 out of the 30 had a poor fitness wellness level. As other half, there is a total of 15 respondents that perceives with no WRLBP. Out of the 15, 1 response had very good fitness wellness level; 8 out of the 15 had good fitness wellness level; 3 out of the 15 had an average fitness wellness score; Lastly, 4 out of the 15 had a fitness wellness score of poor. To correlate fitness wellness to work-related low back pain, Chi-square was used to determine the significant association of the two and found that the null hypothesis was not rejected. Therefore, the study showed that there was no significant association among the two. This means that regardless of how good or poor a person\u27s level of fitness wellness is, it has no effect on the participants\u27 chance of developing work-related low back pain

The khmer software package: enabling efficient nucleotide sequence analysis [version 1; referees: 2 approved, 1 approved with reservations]

The khmer package is a freely available software library for working efficiently with fixed length DNA words, or k-mers. khmer provides implementations of a probabilistic k-mer counting data structure, a compressible De Bruijn graph representation, De Bruijn graph partitioning, and digital normalization. khmer is implemented in C++ and Python, and is freely available under the BSD license at https://github.com/dib-lab/khmer/

khmer v0.8: k-mer counting & filtering FTW

<p>khmer is a library and suite of command line tools for working with DNA sequence. It is primarily aimed at short-read sequencing data such as that produced by the Illumina platform. khmer takes a k-mer-centric approach to sequence analysis, hence the name.</p><p>This is code is v0.8 of khmer.</p><p>The most recent khmer citation is <br></p><p>Crusoe MR, Alameldin HF, Awad S et al. The khmer software package: enabling efficient nucleotide sequence analysis [version 1; referees: 2 approved, 1 approved with reservations]. F1000Research 2015, 4:900 </p><p>(doi: 10.12688/f1000research.6924.1)</p

Data from: Sustained fitness gains and variability in fitness trajectories in the long-term evolution experiment with Escherichia coli

Many populations live in environments subject to frequent biotic and abiotic changes. Nonetheless, it is interesting to ask whether an evolving population's mean fitness can increase indefinitely, and potentially without any limit, even in a constant environment. A recent study showed that fitness trajectories of Escherichia coli populations over 50 000 generations were better described by a power-law model than by a hyperbolic model. According to the power-law model, the rate of fitness gain declines over time but fitness has no upper limit, whereas the hyperbolic model implies a hard limit. Here, we examine whether the previously estimated power-law model predicts the fitness trajectory for an additional 10 000 generations. To that end, we conducted more than 1100 new competitive fitness assays. Consistent with the previous study, the power-law model fits the new data better than the hyperbolic model. We also analysed the variability in fitness among populations, finding subtle, but significant, heterogeneity in mean fitness. Some, but not all, of this variation reflects differences in mutation rate that evolved over time. Taken together, our results imply that both adaptation and divergence can continue indefinitely—or at least for a long time—even in a constant environment

The khmer software package: enabling efficient sequence analysis

<p>A citation handle for the khmer software, v1.0</p

Mutation.Rate.Data

This file contains the mutation rate data from the fluctuation tests in Table S8 in the manuscript