1,721,175 research outputs found
Datasets of the manuscript "Rational design of profile HMMs for sensitive and specific sequence detection with case studies applied to viruses, bacteriophages, and casposons"
No full textDATASETS
Rational design of profile HMMs for sensitive and specific sequence detection with case studies applied to viruses, bacteriophages, and casposons
Liliane S. Oliveira, Alejandro Reyes, Bas E. Dutilh and Arthur Gruber*
* Correspondence: [email protected] (AG); Tel. +55 11 3091 7274
Here we provide different data of Microviridae, Flavivirus and casposons used throughout the work:
Microviridae folder
conserved_HMMs – profile HMMs constructed with TABAJARA in Conservation mode for Microviridae
discriminative_HMMs – profile HMMs constructed with TABAJARA in Discrimination mode for Microviridae
sequences – different sequence datasets and respective multiple sequence alignments
Microviridae_113-seq_training_set.fasta - 113 VP1 sequences covering diversity of the Microviridae family
Microviridae_113-seq.aln – multiple sequence alignment of the 113-protein dataset
Microviridae_1836-seq_testset.fasta - 1,836 sequence dataset covering 1,836 sequences of the major capsid protein (VP1) comprising 501 Alpavirinae sequences, 1,040 Gokushovirinae sequences and 295 Pichovirinae sequences
Microviridae_1866-seq.aln - multiple sequence alignment of the 1,866-protein Microviridae dataset used in the experiment of Figure 4
Flavivirus folder
conserved_HMMs – profile HMMs constructed with TABAJARA in Conservation mode for Flavivirus
discriminative_HMMs – profile HMMs constructed with TABAJARA in Discrimination mode for Flavivirus
full-length – models constructed from full-length protein sequences
short - models constructed from selected short alignment blocks of the protein sequences
sequences – different sequence datasets and respective multiple sequence alignments
Flavivirus_127-seq_training_set.fasta - 127 polyprotein sequences covering species diversity of the genus Flavivirus
Flavivirus_127-seq.aln – multiple sequence alignment of the 127-protein dataset
Flavivirus_6364-seq_testset.fasta - 6,364 sequence dataset covering species diversity of Flavivirus, including 3,919 of dengue virus (DENV), 327 of Zika virus (ZIKV), 63 of yellow fever virus (YFV), and the remaining 2,055 sequences covering other available flaviviruses
Flavivirus_6364-seq.aln - multiple sequence alignment of the 6,364-protein Flavivirus dataset
Casposons folder
casposon_generic_HMMs – profile HMMs constructed with TABAJARA in Discrimination mode for the generic detection of all casposons and discrimination from CRISPRs.
casposon_family_discriminative_HMMs – profile HMMs constructed with TABAJARA in Discrimination mode for the specific discrimination among casposon families and from CRISPRs.
sequences – different sequence datasets and respective multiple sequence alignments
casposons_crisprs.fasta – 106 Cas1 bona fide sequences derived from 52 CRISPRs and 54 casposons
casposon_family_discrimination.aln - multiple sequence alignment of 52 bona fide CRISPR and 54 casposon sequences, with appropriate nomenclature to run TABAJARA for the discrimination of each casposon family.
casposons_crisprs_discrimination.aln - multiple sequence alignment of 52 bona fide CRISPR and 54 casposon sequences, with appropriate nomenclature to run TABAJARA for discrimination of CRISPRs and casposons
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Get PDFWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
A social niche breadth score reveals niche range strategies of generalists and specialists
Get PDFAbstract
Generalists can survive in many environments whereas specialists are restricted to a single environment. Although a classical concept in ecology, niche breadth has remained challenging to quantify for microbes because it depends on an objective definition of the environmental conditions. Here, by defining the environment of a microbe as the community it resides in, we integrated information from over 22 thousand environmental sequencing samples to derive a quantitative measure of the niche, which we call ‘social niche breadth’. At the level of genera, we explored niche range strategies throughout the prokaryotic tree of life. We found that social generalists include opportunists that stochastically dominate local communities, while social specialists are stable but low in abundance. Social generalists have a more diverse and open pan genome than social specialists, but we found no global correlation between social niche breadth and genome size. Instead, we observed two distinct evolutionary strategies, where specialists have relatively small genomes in habitats with low local diversity, but relatively large genomes in habitats with high local diversity. Together, our analysis shines data-driven light on microbial niche range strategies.
Inside this repository
This is the directory structure and code used to generate all data and figures in the paper "A social niche breadth score reveals niche range strategies of generalists and specialists" by F. A. Bastiaan von Meijenfeldt, Paulien Hogeweg, and Bas E. Dutilh. The code was made by F. A. Bastiaan von Meijenfeldt.
The code inside the ./MGnify directory was used to download the MGnify data.
The code inside the ./niche_breadth directory was used to generate all other data and uses the MGnify data.
The code inside the ./figures directory was used to generate all figures.
Each directory in ./MGnify and ./niche_breadth contains a commands.sh that if run, and if source files are present, will generate all content in that directory. No files are written outside the directory. For example running ./MGnify/commands.sh will generate all files within ./MGnify. The generated files are source files for some of the scripts in ./MGnify/2019-08-20_extra and ./MGnify/2019-08-20_extra/commands.sh can now be run to generate all files within. Source files for the ./niche_breadth subdirectories can be from the ./MGnify directory or from other subdirectories within ./niche_breadth.
The ./figures directory and its subdirectories contain *.ipynb Jupyter Notebook files that if run, and source files are present, will generate the vector files that were used as raw input for the final figures.
The file ./figures/mappings.Figure_to_Notebook.txt contains the mapping of the figure to the notebook that was used to generate the figure. In some cases only part of the notebook output was used in the final figures
koamabayili/VECTRON-author-checklist: VECTRON author checklist
No full textWe have done our best to complete the author checklist relating to the use of animals in the hut study. Note that the objective for the hut study was to evaluate the IRS treatment applications for residual efficacy against Anopheles mosquitoes, including the local An. coluzzii mosquito population. Cows were only used to attract mosquitoes into the huts and no tests were carried out directly on the cows. The author checklist is intended for use with studies where experiments are carried out on animals, which is why we have had such difficulty in completing this for the hut study, as many of the questions do not relate to how the cows were used
Author-wise bibliometric analysis based on entropy.
No full textAuthor-wise bibliometric analysis based on entropy.</p
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