Resultados totales (Incluyendo duplicados): 34357
Encontrada(s) 3436 página(s)
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/231577
Dataset. 2021

FASTA SEQUENCES FOR THE DROSOPHILA MELANOGASTER MANUALLY CURATED TRANSPOSABLE ELEMENTS (MCTE) LIBRARY

  • Rech, Gabriel E.
The compressed file contains two files: MCTE.fasta with the consensus TE sequences in fasta format and the MCTE_info.xlsx Excel file with information for every sequence in the MCTE.fasta file. We used the REPET package (v.2.5) (Flutre et al. 2011; Hoede et al. 2014; Quesneville et al. 2005) for performing TE annotations using a manually curated TE (MCTE) library of consensus sequences. Briefly, REPET is composed of two main pipelines, TEdenovo dedicated to de novo detection of TE families and TEannot for the annotation and analysis of TEs in genomic sequences. For the creation of the MCTE library, we first run the REPET (v.2.5) (Flutre et al. 2011; Hoede et al. 2014; Quesneville et al. 2005) TEdenovo pipeline with default parameters on 13 genomes Drosophila melanogaster natural strains. The manual curation of the identified consensuses involved three main procedures: removal of redundant sequences, the manual identification of potentially artifactual sequences and the classification of consensuses into families. Redundant sequences (consensus sequences present in more than one genome) were identified by first running the PASTEClassifier module from PASTEC with default options (Hoede et al. 2014). We also performed similarity clustering, multiple sequence alignments (MSA) of the clusters and generated consensus sequences for each MSA in order to obtain a consensus sequence representative of all the genomes. We manually explored the consensus sequences and their copies using the plotCoverage tool from REPET and discarded consensuses showing mainly a high number of small copies. The assignation of the consensus sequences into families was performed using BLAT (Kent 2002) against the curated canonical sequences of Drosophila TEs from the Berkeley Drosophila Genome Project (BDGP) v.9.4.1 (https://fruitfly.org/p_disrupt/TE.html). When no matches were found, we used RepeatMasker (v.4) (Smit 2015) with the release RepBaseRepeatMaskerEdition-20181026 of the RepBase (Bao et al. 2015)., Manually Curated Transposable Elements (MCTE) library from Drosophila melanogaster. De novo reconstruction was performed using TEdenovo pipeline from REPET package (v.2.5) (Flutre et al. 2011; Hoede et al. 2014; Quesneville et al. 2005). De-novo genome assemblies were sequenced using long-read sequencing technologies (Oxford Nanopore Technologies or Pacific Bioscience)., This file was created in the framework of the ERC grant number H2020-ERC-2014-CoG-647900, funded by the European Commission (https://erc.europa.eu/)., Peer reviewed

Proyecto: EC/H2020/647900
DOI: http://hdl.handle.net/10261/231577
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/231577
HANDLE: http://hdl.handle.net/10261/231577
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/231577
PMID: http://hdl.handle.net/10261/231577
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/231577
Ver en: http://hdl.handle.net/10261/231577
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/231577

Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/231582
Dataset. 2021

RECOMBINATION RATES ACCORDING TO FISTON-LAVIER ET AL. 2010 AND COMERON ET AL. 2012 FOR D. MELANOGASTER GENOME RELEASE 6

  • Rech, Gabriel E.
This file contains genomic coordinates and its recombination rate as determined by the recombination rate calculator (RRC) (Fiston-Lavier et al. 2010) and (Comeron et al. 2012) (http://petrov.stanford.edu/cgi-bin/recombination-rates_updateR5.pl). Such coordinates were originally calculated based on release 5 of D. melanogaster genome so we converted them to release 6 coordinates using the coord_converter.pl script from FlyBase (Gramates et al. 2017). We considered a region to have high recombination rates (HRR) when both recombination estimates were greater than 0., This file contains recombination rates values according to two estimations: Fiston-Lavier et al. 2010 and Comeron et al. 2012 for D. melanogaster genome release 6., This file was created in the framework of the ERC grant number H2020-ERC-2014-CoG-647900, funded by the European Commission (https://erc.europa.eu/)., Peer reviewed

Proyecto: EC/H2020/647900
DOI: http://hdl.handle.net/10261/231582
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/231582
HANDLE: http://hdl.handle.net/10261/231582
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/231582
PMID: http://hdl.handle.net/10261/231582
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/231582
Ver en: http://hdl.handle.net/10261/231582
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/231582

Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/231738
Dataset. 2000

MESOPELAGIC CRUISE, RV GARCÍA DEL CID

  • Hernández León, Santiago
  • CSIC - Unidad de Tecnología Marina (UTM)
MESOPELAGIC Cruise (29GD20000311) carried out on the Research Vessel García del Cid in 2000, Migration and structure of oceanic pelagic systems in the waters of the Canary Islands

Proyecto: //
DOI: http://hdl.handle.net/10261/231738
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/231738
HANDLE: http://hdl.handle.net/10261/231738
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/231738
PMID: http://hdl.handle.net/10261/231738
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/231738
Ver en: http://hdl.handle.net/10261/231738
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/231738

Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/231739
Dataset. 2000

SARDINA CRUISE, RV GARCÍA DEL CID

  • Anadón, Ricardo
  • CSIC - Unidad de Tecnología Marina (UTM)
SARDINA Cruise (29GD20000502) carried out on the Research Vessel García del Cid in 2000, Effect of oceanographic processes on the distribution and feeding of the larvae of Sardina pilchardus, and their consequences on growth, on the Asturian coast.A total of 11 stations were sampled during the daytime (09:00 to 13:00 h) along 4 transects perpendicular to the coast . Vertical profiles of temperature, salinity and fluorescence were taken at each station using a Mark III CTD with a Sea-Tech fluorometer attached to a rosette of 24 Teflon Niskin bottles. Live experimental animals were collected with a triple WP2 net (0.60 m diameter, 200 µm mesh) equipped with 3 l cod-ends. Hauls were made vertically from 200 m to the surface, or from 5 m above the bottom to the surface at the coastal stations. Once on deck, 1 or 2 cod-ends were immediately processed for gut pigment content analysis. Another haul was made and the 3 cod-ends were diluted in a 5 l plastic jar filled with 100 µm-filtered seawater to ensure that the animals remained alive for our experiments. Water used for the incubations was collected with Van Dorn bottles (15 l) from the depth of maximum fluorescence (MFD). Bongo net hauls were performed to collect zooplankton samples for abundance estimations as described in González-Quirós et al. (2004). A bongo net (0.60 m diameter, 200 µm mesh) equipped with calibrated flowmeters was towed obliquely from 200 m to the surface, or from 5 m above the bottom to the surface at coastal stations

Proyecto: //
DOI: http://hdl.handle.net/10261/231739
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/231739
HANDLE: http://hdl.handle.net/10261/231739
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/231739
PMID: http://hdl.handle.net/10261/231739
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/231739
Ver en: http://hdl.handle.net/10261/231739
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/231739

Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/231740
Dataset. 2000

GOLFO CRUISE, RV GARCÍA DEL CID

  • Ruiz Segura, Javier
  • CSIC - Unidad de Tecnología Marina (UTM)
GOLFO Cruise (29GD20000508) carried out on the Research Vessel García del Cid in 2000, Study of the physical and biological processes that affect the Gulf of Cadiz region

Proyecto: //
DOI: http://hdl.handle.net/10261/231740
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/231740
HANDLE: http://hdl.handle.net/10261/231740
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/231740
PMID: http://hdl.handle.net/10261/231740
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/231740
Ver en: http://hdl.handle.net/10261/231740
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/231740

Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/231741
Dataset. 2000

ARO CRUISE, RV GARCÍA DEL CID

  • Sabatés, Ana
  • CSIC - Unidad de Tecnología Marina (UTM)
ARO Cruise (29GD20000530) carried out on the Research Vessel García del Cid in 2000, Multidisciplinary monitoring of a body of water of continental origin from the Rhone and its involvement as a transport mechanism of anchovy larvae.Measurements of basic hydrographic parameters were obtained with a MARK-III Neil Brown CTD at 68 stations arranged in transects that covered the whole continental shelf to beyond the shelf-slope front, from northern shelf to central shelf.At each station, samples of phytoplankton (which includes a component of detritus), zooplankton and anchovy larvae were taken for the determination of fatty acids. For pigment analysis of phytoplankton, 2 L of water collected by Niskin bottles was filtered with low (0.25 bar) positive pressure through Whatman GF/F glass fibre filters that were immediately frozen in liquid N2. Pigment samples were taken between 4 and 30 m depth (surface samples).Zooplankton (>53 μm) was sampled by vertical hauls from 70 m (below deep chlorophyll maximum) to the surface with 40 cm diameter plankton net,Anchovy larvae were sampled by oblique tows using a Bongo net with a 60 cm diameter opening and a mesh size of 333 μm

Proyecto: //
DOI: http://hdl.handle.net/10261/231741
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/231741
HANDLE: http://hdl.handle.net/10261/231741
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/231741
PMID: http://hdl.handle.net/10261/231741
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/231741
Ver en: http://hdl.handle.net/10261/231741
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/231741

Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/231742
Dataset. 2000

ARPA CRUISE, RV GARCÍA DEL CID

  • Lleonart, Jordi
  • CSIC - Unidad de Tecnología Marina (UTM)
ARPA Cruise (29GD20000620) carried out on the Research Vessel García del Cid in 2000, Performing day-night trawls for detection of prawn activity rhythms and underwater photography transects

Proyecto: //
DOI: http://hdl.handle.net/10261/231742
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/231742
HANDLE: http://hdl.handle.net/10261/231742
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/231742
PMID: http://hdl.handle.net/10261/231742
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/231742
Ver en: http://hdl.handle.net/10261/231742
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/231742

Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/231743
Dataset. 2000

NERIT-II CRUISE, RV GARCÍA DEL CID

  • Sardà, Francisco
  • CSIC - Unidad de Tecnología Marina (UTM)
NERIT-II Cruise (29GD20000622) carried out on the Research Vessel García del Cid in 2000, Performing day-night trawls for detection of lobster activity rhythms and underwater photography transects

Proyecto: //
DOI: http://hdl.handle.net/10261/231743
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/231743
HANDLE: http://hdl.handle.net/10261/231743
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/231743
PMID: http://hdl.handle.net/10261/231743
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/231743
Ver en: http://hdl.handle.net/10261/231743
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/231743

Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/231744
Dataset. 2000

CRAC CRUISE, RV GARCÍA DEL CID

  • Font, Jordi
  • CSIC - Unidad de Tecnología Marina (UTM)
CRAC Cruise (29GD20000913) carried out on the Research Vessel García del Cid in 2000, The objective of the campaign is to make precise determinations of sea level using light buoys with GPS antennas at the time of the passage of the altimetric satellites ERS-2 and TOPEX / POSEIDON. As a complement, CTD stations will be made (without taking samples from water) and continuous radial with ADCP and Nu-Shuttle along some of the traces of these satellites

Proyecto: //
DOI: http://hdl.handle.net/10261/231744
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/231744
HANDLE: http://hdl.handle.net/10261/231744
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/231744
PMID: http://hdl.handle.net/10261/231744
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/231744
Ver en: http://hdl.handle.net/10261/231744
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/231744

Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/231745
Dataset. 2001

PRACTICAS-01 CRUISE, RV GARCÍA DEL CID

  • Arístegui, Javier
  • CSIC - Unidad de Tecnología Marina (UTM)
PRACTICAS-01 Cruise (29GD20010206) carried out on the Research Vessel García del Cid in 2001

Proyecto: //
DOI: http://hdl.handle.net/10261/231745
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/231745
HANDLE: http://hdl.handle.net/10261/231745
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/231745
PMID: http://hdl.handle.net/10261/231745
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/231745
Ver en: http://hdl.handle.net/10261/231745
Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/231745

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