Using EMBL‐EBI Services via Web Interface and Programmatically via Web Services

López, Rodrigo; Cowley, Andrew Peter; Li, Weizhong; McWilliam, Hamish

doi:10.1002/0471250953.bi0312s48

Cited by 18 publications

(13 citation statements)

References 31 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…We aligned DNA sequences using muscle 3.8 (Edgar, ) implemented in the EMBL‐EBI server (Lopez et al ., ). Both alignments were combined in a concatenated molecular dataset comprising 2450 bp (Appendix File S3).…”

Section: Methodsmentioning

confidence: 97%

Genus delimitation, biogeography and diversification ofChoristoneuraLederer (Lepidoptera: Tortricidae) based on molecular evidence

Fagua

Condamine

Dombroskie

et al. 2018

Systematic Entomology

View full text Add to dashboard Cite

Widely known for pest species that include major modulators of temperate forests, the genus Choristoneura is part of the species-rich tribe Archipini of leafroller moths (Tortricidae). Delimitation of the genus has remained unresolved because no phylogeny has included species endemic to Africa and studies have often omitted the type species of the genus. Further taxonomic confusion has been generated by the transfer of Archips occidentalis (Walsingham) to Choristoneura, creating a homonym with Choristoneura occidentalis Freeman, an important defoliator of North American forests. To define the limits of the genus, we reconstructed a phylogeny using DNA sequences for mitochondrial cytochrome oxidase subunit I and nuclear ribosomal 28S genes. Our ingroup included 23 Choristoneura species-level taxa, complemented by a large sample of outgroups comprising 82 species of Archipini and other Tortricidae. We generated a time-calibrated tree using fossil and secondary calibrations and we inferred biogeographic and diversification processes in Choristoneura. Our analysis recovered the genus as polyphyletic, with Archips occidentalis, Choristoneura simonyi and Choristoneura evanidana excluded from the main clade. Based on the recovered phylogenies and a redefinition, we restrict Choristoneura primarily to species with a northern hemisphere distribution. Our analysis supports A. occidentalis as the sister group of Cacoecimorpha pronubana, C. simonyi as the sister of 'Xenotemna' pallorana, and C. evanidana as the sister of Archips purpurana. A new combination is proposed: Archips evanidana comb.n.; the availability of 'Xenotemna' as a valid name is discussed and A. occidentalis is considered as an orphaned name within the Archipini. We found support for a Holarctic origin of Choristoneura about 23 Ma, followed by early divergence in the Palearctic region. The main divergence occurred at 16 Ma, with one clade in the Nearctic and another in the Palearctic. Subsequent cladogenetic events were synchronous and related to herbivorous specialization, with each clade divided into coniferophagous and polyphagous lineages. Their specialization as conifer feeders temporally matched the expansion of boreal forest during the Miocene. or Zelotherses. Our phylogenetic analysis indicates the closest relationship to Cacoecimorpha; however, we need a larger sample of African and Far East Archipini to corroborate the hypothesis.

show abstract

Section: Methodsmentioning

confidence: 97%

Genus delimitation, biogeography and diversification ofChoristoneuraLederer (Lepidoptera: Tortricidae) based on molecular evidence

Fagua

Condamine

Dombroskie

et al. 2018

Systematic Entomology

View full text Add to dashboard Cite

show abstract

“…Fungal proteins, especially of the order Polyporales were also used to support gene prediction, by providing protein homology evidence. The contigs predicted by MAKER2 were analyzed with GoFeat [23] using the following databases: UNIPROT [24] , INTERPRO [25] , PFAM [26] , SEED [27] , NCBI [28] , EMBL [29] , KEGG [30] . CAZymes were identified with dbCAN version 5.0 [31] .…”

Section: Experimental Design Materials and Methodsmentioning

confidence: 99%

Draft genome sequence of Trametes villosa (Sw.) Kreisel CCMB561, a tropical white-rot Basidiomycota from the semiarid region of Brazil

et al. 2018

View full text Add to dashboard Cite

Herein, we present the draft genome of Trametes villosa isolate CCMB561, a wood-decaying Basidiomycota commonly found in tropical semiarid climate. The genome assembly was 57.98 Mb in size with an L50 of 691. A total of 16,711 putative protein-encoding genes was predicted, including 590 genes coding for carbohydrate-active enzymes (CAZy), directly involved in the decomposition of lignocellulosic materials. This is the first genome of this species of high interest in bioenergy research. The draft genome of Trametes villosa isolate CCMB561 will provide an important resource for future investigations in biofuel production, bioremediation and other green technologies.

show abstract

“…EMBL-EBI offers helpdesk support and training courses for the use of the tool services provided by the framework. General help, FAQ pages, tutorials and example protocols ( 16 ) are available for using the services via web browser interfaces and sample clients for Web Services. A brief guide to Web Services technologies is also provided for those wishing to learn more and develop their own client programs ( https://www.ebi.ac.uk/Tools/webservices/tutorials/00_contents ).…”

Section: The Tools Frameworkmentioning

confidence: 99%

“…The framework is used by academic and industry scientists, and in 2014 handled roughly 110 million analysis jobs, up from 65 million in 2013. Help pages, tutorials and user guides (available as protocols ( 16 )) are provided, together with training courses and helpdesk support. Continued feedback from the biological community, collaboration with bioinformatics tools and data providers and comprehensive metrics analysis helps to drive improvements to the accessibility and quality of the services.…”

Section: Introductionmentioning

confidence: 99%

The EMBL-EBI bioinformatics web and programmatic tools framework

et al. 2015

Self Cite

View full text Add to dashboard Cite

Since 2009 the EMBL-EBI Job Dispatcher framework has provided free access to a range of mainstream sequence analysis applications. These include sequence similarity search services (https://www.ebi.ac.uk/Tools/sss/) such as BLAST, FASTA and PSI-Search, multiple sequence alignment tools (https://www.ebi.ac.uk/Tools/msa/) such as Clustal Omega, MAFFT and T-Coffee, and other sequence analysis tools (https://www.ebi.ac.uk/Tools/pfa/) such as InterProScan. Through these services users can search mainstream sequence databases such as ENA, UniProt and Ensembl Genomes, utilising a uniform web interface or systematically through Web Services interfaces (https://www.ebi.ac.uk/Tools/webservices/) using common programming languages, and obtain enriched results with novel visualisations. Integration with EBI Search (https://www.ebi.ac.uk/ebisearch/) and the dbfetch retrieval service (https://www.ebi.ac.uk/Tools/dbfetch/) further expands the usefulness of the framework. New tools and updates such as NCBI BLAST+, InterProScan 5 and PfamScan, new categories such as RNA analysis tools (https://www.ebi.ac.uk/Tools/rna/), new databases such as ENA non-coding, WormBase ParaSite, Pfam and Rfam, and new workflow methods, together with the retirement of depreciated services, ensure that the framework remains relevant to today's biological community.

show abstract

Using EMBL‐EBI Services via Web Interface and Programmatically via Web Services

Cited by 18 publications

References 31 publications

Genus delimitation, biogeography and diversification ofChoristoneuraLederer (Lepidoptera: Tortricidae) based on molecular evidence

Genus delimitation, biogeography and diversification ofChoristoneuraLederer (Lepidoptera: Tortricidae) based on molecular evidence

Draft genome sequence of Trametes villosa (Sw.) Kreisel CCMB561, a tropical white-rot Basidiomycota from the semiarid region of Brazil

The EMBL-EBI bioinformatics web and programmatic tools framework

Contact Info

Product

Resources

About