1,786 research outputs found
Alternate version of File S3 from Linheiro & Bergman 2012
No full text<p>An alternative version of File S3 from Linheiro & Bergman 2012 that encodes the number of DGRP strains in which the TE insertion is found in the score field of the .bed file. The data in this alternate version of File S3 are based on the revised dataset from Linheiro & Bergman 2012 posted here: http://dx.doi.org/10.6084/m9.figshare.683836</p
Revised version of File S6 from Linheiro & Bergman 2012
No full text<p>A revised version of File S6 from Linheiro & Bergman 2012 that corrects the number of reads supporting each target site duplication.</p>
<p>The originally reported data file provided incorrect read support counts based only on the first strain in which the TE insertion was identified, rather than the total number of read counts from all strains merge across the dataset.</p>
<p>For 1,606 TE insertions that are present in more than one strain identified using Illumina sequencing, the corrected number of reads supporting the TE insertion is higher than originally reported.</p>
<p>The location, strand and TE family for all 8,024 TE insertion sites identified using Illumina seqeuncing in Linheiro & Bergman 2012 is unchanged.</p>
<p>None of the main conclusions of Linheiro & Bergman 2012 are affected by this error.</p
Revised version of File S1 from Linheiro & Bergman 2012
No full text<p>A revised version of File S1 from Linheiro & Bergman 2012 that corrects the number of reads supporting each target site duplication.</p>
<p>The originally reported data file provided incorrect read support counts based only on the first strain in which the TE insertion was identified, rather than the total number of read counts from all strains merged across the entire dataset.</p>
<p>For 461 TE insertions that are present in more than one strain identified using 454 sequencing, the corrected number of reads supporting the TE insertion is higher than originally reported.</p>
<p>The location, strand and TE family for 3,379 out of 3,386 TE insertion sites identified using 454 sequencing in Linheiro & Bergman 2012 is unchanged. For 7 out of the 3,386 TE insertions identified using 454 sequencing, properly merging reads across strains led to differences in location, strand or TE family predicted.</p>
<p>None of the main conclusions of Linheiro & Bergman 2012 are affected by this error.</p
Revised version of File S4 from Linheiro & Bergman 2012
No full text<p>A revised version of File S4 from Linheiro & Bergman 2012 that corrects the number of reads supporting each target site duplication.</p>
<p>The originally reported data file provided incorrect read support counts based only on the first strain in which the TE insertion was identified, rather than the total number of read counts from all strains merged across the entire dataset.</p>
<p>For 1,606 TE insertions that are present in more than one strain identified using Illumina sequencing, the corrected number of reads supporting the TE insertion is higher than originally reported.</p>
<p>The location, strand and TE family for all 8,024 TE insertion sites identified using Illumina sequencing in Linheiro & Bergman 2012 is unchanged.</p>
<p>None of the main conclusions of Linheiro & Bergman 2012 are affected by this error.</p
Strain-specific annotation files for data in File S4 from Linheiro & Bergman 2012
No full text<p>Data in File S4 from Linheiro & Bergman 2012 are merged across all strains in the DGRP sample. This archive provides .bed files for individual strains with read support in the score field. The strain-specific data here are based on the revised Illumina dataset from Linheiro & Bergman 2012 posted here: http://dx.doi.org/10.6084/m9.figshare.683834.</p>
<p>The union of these strain specific .bed files differs slightly from the merged .bed file corresponding to File S4 because of overlapping TE insertions sites. In the merging process, 3 TE insertion sites supported by a total of 23 reads were eliminated.</p
Revised version of File S3 from Linheiro & Bergman 2012
No full text<p>A revised version of File S3 from Linheiro & Bergman 2012 that corrects the number of reads supporting each target site duplication.</p>
<p>The originally reported data file provided incorrect read support counts based only on the first strain in which the TE insertion was identified, rather than the total number of read counts from all strains merged across the entire dataset.</p>
<p>For 461 TE insertions that are present in more than one strain identified using 454 sequencing, the corrected number of reads supporting the TE insertion is higher than originally reported.</p>
<p>The location, strand and TE family for 3,379 out of 3,386 TE insertion sites identified using 454 sequencing in Linheiro & Bergman 2012 is unchanged. For 7 out of the 3,386 TE insertions identified using 454 sequencing, properly merging reads across strains led to differences in location, strand or TE family predicted.</p>
<p>None of the main conclusions of Linheiro & Bergman 2012 are affected by this error.</p
Whole genome resequencing reveals natural target site preferences of transposable elements in Drosophila melanogaster
No full textTransposable elements are mobile DNA sequences that integrate into host genomes using diverse mechanisms with varying degrees of target site specificity. While the target site preferences of some engineered transposable elements are well studied, the natural target preferences of most transposable elements are poorly characterized. Using population genomic resequencing data from 166 strains of Drosophila melanogaster, we identified over 8,000 new insertion sites not present in the reference genome sequence that we used to decode the natural target preferences of 22 families of transposable element in this species. We found that terminal inverted repeat transposon and long terminal repeat retrotransposon families present clade-specific target site duplications and target site sequence motifs. Additionally, we found that the sequence motifs at transposable element target sites are always palindromes that extend beyond the target site duplication. Our results demonstrate the utility of population genomics data for high-throughput inference of transposable element targeting preferences in the wild and establish general rules for terminal inverted repeat transposon and long terminal repeat retrotransposon target site selection in eukaryotic genomes. © 2012 Linheiro, Bergman
Bilingual acquisition data: Dative Alternation_DA-L2 Adult dataset
No full textThis dataset is the result of the research carried out by Silvia Sánchez Calderón (UNED) and Raquel Fernández Fuertes (UVa) in the frame of the Research Group UVALAL (University of Valladolid Language Acquisition Lab, https://uvalal.uva.es/) whose Principal Investigator is Raquel Fernández Fuertes. In this project, the research is conducted on the second language (L2) acquisition of English Dative Alternation (DA) constructions by adult learners whose first language (L1) is Spanish. The results are compared to a control group of L1 English adults. An Acceptability Judgment Task (AJT) was designed for both groups to address grammaticality, sentence structure and word order of the two English DA structures.
The two DA structures under analysis involve, on the one hand, prepositional to-datives that alternate as Double Object Constructions (DOCs) (1) and, on the other hand, prepositional for-datives that alternate as DOCs (2). The main aim of this project is to explore the role played by the L2 English learners' L1 in their sensitivity towards the two syntactic variants, with a particular emphasis on the potential crosslinguistic influence effects (or lack thereof) from Spanish into English and the Universal Grammar (UG) effect on their acquisition.UVALAL1. GENERAL INFORMATION 1.1. Title of dataset 1.2. Author information 1.2.1. PI and co-PI 1.2.2. Lab 1.2.3 People involved in the data collection and the tasks design 1.3. Objectives 1.4. Funding sources 1.5. Citing information 2. ACCESS INFORMATION 2.1. Licenses or restrictions 2.2. Publications 3. METHODOLOGICAL INFORMATION 3.1. The participants 3.2. The experimental task: an Acceptability Judgment Task 3.3. Data extraction procedure 3.4. Data classification procedure: variables 4. DATA 4.1. Database 4.2. Last update 5. RELATED DATASETSSpanish Ministry of Science, Innovation and Universities and European Regional Development Fund (ERDF) [PGC2018-097693-B-I00],Regional Government of Castile and León (Spain) and ERDF [VA009P17
Os ventos da América Latina, por raquel ochoa
Get PDFThis article analyzes The Wind of Others (2012), by
Raquel Ochoa, a contemporary Portuguese author
who presents a set of travel chronicles through Cen-
tral and South America, from a feminine perspecti-
ve in search of identity and questioning the native
Other. Passionate about writing and travelling, the
author wanders aimlessly like the wind through
the Andes from Costa Rica to Patagonia in Argen-
tina to emerge in the local culture away from the
more commercial tours. As part of travel literature,
the search for the Other(s) reveals alterity and traces
a critical portrait of the plight of the peoples of Latin
America, which result from the processes of coloni-
zation and globalization. The personal encounters
and adventures blend in a literature of the senses re-
vealing the landscapes, the peoples and the winds
of Latin America from a transatlantic perspective.Este artigo analisa O Vento dos Outros (2012), de
Raquel Ochoa, uma autora Portuguesa contem-
porânea que apresenta um conjunto de crónicas de
viagem da América Central à América do Sul, numa
narrativa de olhar feminista em questionamento
identitário com o Outro local. Apaixonada pela escri-
ta e pelas viagens, a autora vagueia sem rumo como
o vento pelos Andes desde a Costa Rica até à Pata-
gónia na Argentina com o objetivo de uma imersão
cultural afastando-se de um périplo mais comercial.
Inserindo-se na literatura de viagens a procura do(s)
outro(s) revela a alteridade e traça um retrato crítico
das difíceis condições de vida dos povos da América
Latina, resultantes dos processos de colonização e
de globalização. Os encontros e aventuras pessoais
misturam-se numa literatura dos sentidos revelan-
do as paisagens, as gentes e os ventos da Améri-
ca Latina a partir de uma perspetiva transatlântica
CView: test case dataset
No full textSummary
All North American subtype B gp120 sequences, verified to be CCR5-using sequences (n = 636), were downloaded from the Los Alamos HIV sequence database in aligned fasta format [1]. These were loaded into CView, using the “Load (fasta)” option of the “All Sequences” menu, following which they were saved in unaligned format using the “Save (unaligned)” option of the “All Sequences” menu. Additionally, the titles of these sequences were saved to a separate file using the “Save (titles)” option. This was repeated for CXCR4-using sequences (n = 76). In order to make sites directly comparable between the two sets of unaligned sequences, they were combined into a single file and aligned using MUSCLE [2].
This alignment was used in the test case example of our CView paper [3] titled “CView: A network based tool for enhanced alignment visualization” (view).
The CView project page is located at: https://sourceforge.net/projects/cview/
A poster sumarization presented at ISMB 2022 is available here.
Tutorials
1. A demonstration of CView usage in the form of an mp4 movie is available here.
2. A demonstration of how variants can be identified using CView is available here.
Related software to this project are:
1. CStone
2. CSReadGen
3. CView <
4. ChimSim
5. TVScript
General details of the project are available here.
References
1. Kuiken C, Korber B, Shafer RW. HIV Sequence Databases. AIDS Rev. 2003;5: 52. Available: /pmc/articles/PMC2613779/
2. Edgar R. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32: 1792–1797. doi:10.1093/NAR/GKH340
3. Linheiro, R., Sabatino, S., LoboID, D., & ArcherID, J. (2022). CView: A network based tool for enhanced alignment visualization. PLOS ONE, 17(6), e0259726. https://doi.org/10.1371/JOURNAL.PONE.0259726
| linkedIn . web . orcid |
| linheiro . web . orcid |---| sabatino . web . orcid |---| lobo . web . orcid |---| archer . web . orcid |This work was funded by the project NORTE-01-0246-FEDER-000063, supported by Norte Portugal Regional Operational Programme (NORTE2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF), and by research funding from the project under the references PTDC/BIA-EVF/29115/2017 and POCI-01-0145-FEDER-029115 co-funded by Operational Competitiveness and Internationalization Program, Portugal 2020 and the European Union via the European Regional Development Fund (ERDF), and by National Funds through FCT. DL was supported by FCT through a PhD grant with the reference PD/BD/132403/2017. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. FCT URL: https://www.fct.pt/
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