PhylomeDB: Difference between revisions
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}}'''PhylomeDB''' is a public database for complete catalogs pf gene phylogenies ([[Phylogenetics|phylomes]])<ref name="pmid17962297">{{cite journal |last=Huerta-Cepas |
}}'''PhylomeDB''' is a public database for complete catalogs pf gene phylogenies ([[Phylogenetics|phylomes]])<ref name="pmid17962297">{{cite journal |last=Huerta-Cepas, J|authorlink=|author2=Bueno, A |author3=Dopazo, J |author4=Gabaldón, T |date=Jan 2008|title=PhylomeDB: a database for genome-wide collections of gene phylogenies|journal = Nucleic Acids Res.|volume=36|issue=Database issue|pages=D491-6|publisher= |location = England| issn = | pmid = 17962297|doi = 10.1093/nar/gkm899| bibcode = | oclc =| id = | url = | pmc =2238872 | format = | accessdate = | laysummary = | laysource = | laydate = | quote = }}</ref> <ref name="pmid21075798">{{cite journal |last=Huerta-Cepas|first=Jaime|authorlink=|author2=Capella-Gutierrez, S|author3=Pryszcz, LP|author4=Denisov, I|author5=Kormes, D|author6=Marcet-Houben, M|author4=Gabaldón, T|date=Jan 2011|title=PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions.|journal = Nucleic Acids Res.|volume=39|issue=Database issue|pages=D556-60|publisher= |location = England| issn = | pmid = 21075798|doi = 10.1093/nar/gkq1109| bibcode = | oclc =| id = | url = | pmc =3013701 | format = | accessdate = | laysummary = | laysource = | laydate = | quote = }}</ref> <ref name="pmid24275491">{{cite journal |last=Huerta-Cepas|first=Jaime|authorlink=|author2=Capella-Gutierrez, S|author3=Pryszcz, LP|author4=Marcet-Houben, M|author5=Gabaldón, T|date=Jan 2014|title=PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome.|journal = Nucleic Acids Res.|volume=42|issue=Database issue|pages=D897-902|publisher= |location = England| issn = | pmid = 24275491|doi = 10.1093/nar/gkt1177 | bibcode = | oclc =| id = | url = | pmc =3964985 | format = | accessdate = | laysummary = | laysource = | laydate = | quote = }}</ref>. It allows users to interactively explore the evolutionary history of genes through the visualization of phylogenetic trees and multiple sequence alignments. Moreover, phylomeDB provides genome-wide orthology and paralogy predictions which are based on the analysis of the phylogenetic trees. The automated pipeline used to reconstruct trees aims at providing a high-quality phylogenetic analysis of different genomes, including Maximum Likelihood tree inference, alignment trimming <ref name="pmid19505945">{{cite journal |last=Capella-Gutierrez, S|author2= Silla-Martínez, JM|author3=Gabaldón, T |date=Aug 2009|title=trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses.|journal = Bioinformatics. |volume=25(15)|issue=Database issue|pages=1972-3|publisher= |location = | issn = | pmid = 19505945|doi =10.1093/bioinformatics/btp348| bibcode = | oclc =| id = | url = | pmc = 2712344 | format = | accessdate = | laysummary = | laysource = | laydate = | quote = }}</ref> and evolutionary model testing. |
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PhylomeDB includes also a public download section with the complete set of trees, alignments and orthology predictions, as well as a web API that faciliates cross linking trees from external sources. Finally, phylomeDB provides an advanced tree visualization interface based on the ETE toolkit, which integrates tree topologies, taxonomic information, domain mapping and alignment visualization in a single and interactive tree image. |
PhylomeDB includes also a public download section with the complete set of trees, alignments and orthology predictions, as well as a web API that faciliates cross linking trees from external sources. Finally, phylomeDB provides an advanced tree visualization interface based on the ETE toolkit<ref name="pmid20070885">{{cite journal |last=Huerta-Cepas, J|author2= Dopazo, J|author3=Gabaldón, T |date=Jan 2010|title=ETE: a python Environment for Tree Exploration.|journal = BMC Bioinformatics. |volume=13|issue=Database issue|pages=11:24|publisher= |location = | issn = | pmid = 20070885|doi =10.1186/1471-2105-11-24| bibcode = | oclc =| id = | url = | pmc = 2820433 | format = | accessdate = | laysummary = | laysource = | laydate = | quote = }}</ref>, which integrates tree topologies, taxonomic information, domain mapping and alignment visualization in a single and interactive tree image. |
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==What is new in phylomeDB 4?== |
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We updated the tree searching engine to provide a gene-centric view of all phylomeDB resources. Thus, after a protein or gene search, all the available trees in phylomeDB are listed and organized by phylome and tree type. Users can switch among all available seed and collateral trees without missing the focus on the searched protein or gene. |
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In phylomeDB v4 all the information available for each tree is now shown using an integrated layout in which tree topology, taxonomy data, alignments and domain annotations, and event-age (phylostratigraphy) information are rendered in the same figure using the newest visualization features provided by the ETE toolkit v2.2: |
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i) PFAM domains, have been mapped to each alignment in our database and are now displayed in a compact panel at the right side of the tree (Figure 1e). For each sequence, domains and their names are shown, they can be clicked to obtain a short description and the external link to PFAM (Figure 1i). Protein regions not mapped to domains are shown using the standard amino acid color codes, while gap regions are represented by a flat line. |
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ii) A taxonomy-information panel has been added to the right side of every tree that allows to highlight the main taxonomic clades present within each gene tree. Information on the estimated the relative age (i.e. phylostratygraphy) of each tree node �(18)�, as well as extended taxonomic and GO functional information, is provided through the contextual menu available by clicking. |
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iii) Tree images have been also simplified to improve readability. Mappings and/or cross-linking to general and organism-oriented databases has been extended to include the major Arabidopsis thaliana sequence database TAIR�, Drosophila’s Flybase, as well as the Ascomycete-based genome database Genolevures. By default a single sequence identifier is shown on the tree, prioritizing those that are more suited for human interpretation, but this can be can be adjusted through the tree editing menu. A conversion table among PhylomeDB unique identifiers and other identifiers is provided in the download section. |
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iv) Speciation and duplication events are indicated using different node colors andbranch support values are now automatically highlighted for lowly supported partitions using a transparent red bubble inversely proportional to the branch bootstrap or aLRT value. |
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v) Internal tree searches can be performed for any of the annotated node attributes while links to other databases are provided through the contextual menu of the tree browser that appear when clicking any node . |
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News on the tree action menu |
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Users can download relevant data, including the whole database, a specific phylome or, from the tree entry page, the relevant data corresponding to that tree. In this new release we have implemented the posibibility to download orthology predictions from a tree in the recently-developed OrthoXML standard format, in addition to a tabulated format. |
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News on the web-API |
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Finally, the web-based linking API has been improved and it now allows for direct links to trees and phylomes as well as highlighting custom nodes within a tree topology . The URL format used by the API is detailed in Table 1. |
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==Quest for Orthologs== |
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==See also== |
==See also== |
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Revision as of 12:52, 11 February 2015
| PhylomeDB logo.png | |
| Content | |
|---|---|
| Description | genome-wide collections of gene phylogenies. |
| Contact | |
| Laboratory | Comparative Genomics Group, Centre for Genomic Regulation (CRG), Barcelona, Spain. |
| Authors | Salvador Capella-Gutierrez, Leszek Pryszcz, Marina Marcet-Houben, Ernst Thür, Laia Carreté and Toni Gabaldón |
| Primary citation | Huerta-Cepas & al. (2008)[1] |
| Release date | 2007 |
| Access | |
| Website | http://phylomedb.org |
PhylomeDB is a public database for complete catalogs pf gene phylogenies (phylomes)[1] [2] [3]. It allows users to interactively explore the evolutionary history of genes through the visualization of phylogenetic trees and multiple sequence alignments. Moreover, phylomeDB provides genome-wide orthology and paralogy predictions which are based on the analysis of the phylogenetic trees. The automated pipeline used to reconstruct trees aims at providing a high-quality phylogenetic analysis of different genomes, including Maximum Likelihood tree inference, alignment trimming [4] and evolutionary model testing.
PhylomeDB includes also a public download section with the complete set of trees, alignments and orthology predictions, as well as a web API that faciliates cross linking trees from external sources. Finally, phylomeDB provides an advanced tree visualization interface based on the ETE toolkit[5], which integrates tree topologies, taxonomic information, domain mapping and alignment visualization in a single and interactive tree image.
What is new in phylomeDB 4?
We updated the tree searching engine to provide a gene-centric view of all phylomeDB resources. Thus, after a protein or gene search, all the available trees in phylomeDB are listed and organized by phylome and tree type. Users can switch among all available seed and collateral trees without missing the focus on the searched protein or gene.
In phylomeDB v4 all the information available for each tree is now shown using an integrated layout in which tree topology, taxonomy data, alignments and domain annotations, and event-age (phylostratigraphy) information are rendered in the same figure using the newest visualization features provided by the ETE toolkit v2.2:
i) PFAM domains, have been mapped to each alignment in our database and are now displayed in a compact panel at the right side of the tree (Figure 1e). For each sequence, domains and their names are shown, they can be clicked to obtain a short description and the external link to PFAM (Figure 1i). Protein regions not mapped to domains are shown using the standard amino acid color codes, while gap regions are represented by a flat line.
ii) A taxonomy-information panel has been added to the right side of every tree that allows to highlight the main taxonomic clades present within each gene tree. Information on the estimated the relative age (i.e. phylostratygraphy) of each tree node �(18)�, as well as extended taxonomic and GO functional information, is provided through the contextual menu available by clicking.
iii) Tree images have been also simplified to improve readability. Mappings and/or cross-linking to general and organism-oriented databases has been extended to include the major Arabidopsis thaliana sequence database TAIR�, Drosophila’s Flybase, as well as the Ascomycete-based genome database Genolevures. By default a single sequence identifier is shown on the tree, prioritizing those that are more suited for human interpretation, but this can be can be adjusted through the tree editing menu. A conversion table among PhylomeDB unique identifiers and other identifiers is provided in the download section.
iv) Speciation and duplication events are indicated using different node colors andbranch support values are now automatically highlighted for lowly supported partitions using a transparent red bubble inversely proportional to the branch bootstrap or aLRT value.
v) Internal tree searches can be performed for any of the annotated node attributes while links to other databases are provided through the contextual menu of the tree browser that appear when clicking any node .
News on the tree action menu
Users can download relevant data, including the whole database, a specific phylome or, from the tree entry page, the relevant data corresponding to that tree. In this new release we have implemented the posibibility to download orthology predictions from a tree in the recently-developed OrthoXML standard format, in addition to a tabulated format.
News on the web-API
Finally, the web-based linking API has been improved and it now allows for direct links to trees and phylomes as well as highlighting custom nodes within a tree topology . The URL format used by the API is detailed in Table 1.
Quest for Orthologs
See also
References
- ^ a b Huerta-Cepas, J; Bueno, A; Dopazo, J; Gabaldón, T (Jan 2008). "PhylomeDB: a database for genome-wide collections of gene phylogenies". Nucleic Acids Res. 36 (Database issue). England: D491-6. doi:10.1093/nar/gkm899. PMC 2238872. PMID 17962297.
{{cite journal}}: Cite has empty unknown parameters:|laysummary=,|laydate=, and|laysource=(help) - ^ Huerta-Cepas, Jaime; Capella-Gutierrez, S; Pryszcz, LP; Gabaldón, T; Kormes, D; Marcet-Houben, M (Jan 2011). "PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions". Nucleic Acids Res. 39 (Database issue). England: D556-60. doi:10.1093/nar/gkq1109. PMC 3013701. PMID 21075798.
{{cite journal}}: Cite has empty unknown parameters:|laydate=,|laysource=, and|laysummary=(help) - ^ Huerta-Cepas, Jaime; Capella-Gutierrez, S; Pryszcz, LP; Marcet-Houben, M; Gabaldón, T (Jan 2014). "PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome". Nucleic Acids Res. 42 (Database issue). England: D897-902. doi:10.1093/nar/gkt1177. PMC 3964985. PMID 24275491.
{{cite journal}}: Cite has empty unknown parameters:|laydate=,|laysource=, and|laysummary=(help) - ^ Capella-Gutierrez, S; Silla-Martínez, JM; Gabaldón, T (Aug 2009). "trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses". Bioinformatics. 25(15) (Database issue): 1972–3. doi:10.1093/bioinformatics/btp348. PMC 2712344. PMID 19505945.
{{cite journal}}: Cite has empty unknown parameters:|laydate=,|laysummary=, and|laysource=(help) - ^ Huerta-Cepas, J; Dopazo, J; Gabaldón, T (Jan 2010). "ETE: a python Environment for Tree Exploration". BMC Bioinformatics. 13 (Database issue): 11:24. doi:10.1186/1471-2105-11-24. PMC 2820433. PMID 20070885.
{{cite journal}}: Cite has empty unknown parameters:|laydate=,|laysummary=, and|laysource=(help)CS1 maint: unflagged free DOI (link)
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