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TreeFam: a curated database of phylogenetic trees of animal gene families

H. Li
2006 Nucleic Acids Research  
TreeFam is a database of phylogenetic trees of gene families found in animals.  ...  Release 1.1 of TreeFam contains curated trees for 690 families 25 and automatically generated trees for another 11 646 families.  ...  As a result, we decided to develop TreeFam, a database of curated 45 phylogenetic trees of all animal gene families.  ... 
doi:10.1093/nar/gkj118 pmid:16381935 pmcid:PMC1347480 fatcat:f5pvljm3brbdbm3f2dnu6io3vm

TreeFam: 2008 Update

J. Ruan, H. Li, Z. Chen, A. Coghlan, L. J. M. Coin, Y. Guo, J.-K. Heriche, Y. Hu, K. Kristiansen, R. Li, T. Liu, A. Moses (+7 others)
2007 Nucleic Acids Research  
TreeFam (http://www.treefam.org) was developed to provide curated phylogenetic trees for all animal gene families, as well as orthologue and paralogue assignments.  ...  Release 4.0 of TreeFam contains curated trees for 1314 families and automatically generated trees for another 14 351 families.  ...  TreeFam aims to be a curated database of phylogenetic trees of all animal gene families, focusing on gene sets from animals with completely sequenced genomes.  ... 
doi:10.1093/nar/gkm1005 pmid:18056084 pmcid:PMC2238856 fatcat:5bttgct3jrbcbfubwwepdg3fwe

Berkeley PHOG: PhyloFacts orthology group prediction web server

Ruchira S. Datta, Christopher Meacham, Bushra Samad, Christoph Neyer, Kimmen Sjölander
2009 Nucleic Acids Research  
Results on a benchmark dataset from the TreeFam-A manually curated orthology database show that PHOG provides a combination of high recall and precision competitive with both InParanoid and OrthoMCL, and  ...  Ortholog detection is essential in functional annotation of genomes, with applications to phylogenetic tree construction, prediction of protein-protein interaction and other bioinformatics tasks.  ...  FUNDING PECASE Award (grant number 0238311 to K.S.) from the National Science Foundation, National Institutes of Health (grant number R01HG02769 to K.S.) and Microbial Genome Sequencing Program of the  ... 
doi:10.1093/nar/gkp373 pmid:19435885 pmcid:PMC2703887 fatcat:3y57ur55lvh3ffulsy3xnm4rei

Orthology prediction methods: A quality assessment using curated protein families

Kalliopi Trachana, Tomas A. Larsson, Sean Powell, Wei-Hua Chen, Tobias Doerks, Jean Muller, Peer Bork
2011 Bioessays  
We used 70 manually curated families to analyze the performance of five public methods in Metazoa.  ...  and should be tackled by a broad scientific community.  ...  Acknowledgments We would like to thank the OrthoDB team for providing us with a customized dataset.  ... 
doi:10.1002/bies.201100062 pmid:21853451 pmcid:PMC3193375 fatcat:5hkwdtl77nehrjs72vlm2fxpnu

Overview and comparison of ortholog databases

Andrey Alexeyenko, Julia Lindberg, Åsa Pérez-Bercoff, Erik L.L. Sonnhammer
2006 Drug Discovery Today : Technologies  
A large number of resources now exist, each with its own idiosyncrasies. The goal of this review is to compare their contents and clarify which database is most suited for a certain task.  ...  TreeFam is a manually curated database of trees with genes from animal taxa [20] .  ...  Some of the trees were manually curated to construct the TreeFam-A database, which is more reliable. In release 1.1, TreeFam-A contained 690 families and TreeFam-B 11646.  ... 
doi:10.1016/j.ddtec.2006.06.002 pmid:24980400 fatcat:2rw37btp4nfthavz3zsjlcp3mq

The quest for orthologs: finding the corresponding gene across genomes

Arnold Kuzniar, Roeland C.H.J. van Ham, Sándor Pongor, Jack A.M. Leunissen
2008 Trends in Genetics  
TreeFam TreFam is a database of curated (TreeFam-A) and automatically constructed (TreeFam-B) animal gene families, phylogenetic trees, inferred orthologs and paralogs for fully sequenced animal genomes  ...  In summary, treebased methods provide phylogenetic resolution at multiple levels of a gene tree and are suitable to infer orthologs and paralogs from any protein (domain) family database available.  ... 
doi:10.1016/j.tig.2008.08.009 pmid:18819722 fatcat:4w6qrixl7naw7aoqko73vruavq

2R and remodeling of vertebrate signal transduction engine

Lukasz Huminiecki, Carl Heldin
2010 BMC Biology  
Whole genome duplication (WGD) is a special case of gene duplication, observed rarely in animals, whereby all genes duplicate simultaneously through polyploidisation.  ...  Two rounds of WGD (2R-WGD) occurred at the base of vertebrates, giving rise to an enormous wave of genetic novelty, but a systematic analysis of functional consequences of this event has not yet been performed  ...  Systems Biology to conduct interdisciplinary research on the molecular evolution of animal signalling.  ... 
doi:10.1186/1741-7007-8-146 pmid:21144020 pmcid:PMC3238295 fatcat:xfrayzvsrfhr5nkuhooss437h4

A Phylogeny-Based Benchmarking Test for Orthology Inference Reveals the Limitations of Function-Based Validation

Kalliopi Trachana, Kristoffer Forslund, Tomas Larsson, Sean Powell, Tobias Doerks, Christian von Mering, Peer Bork, Maria Anisimova
2014 PLoS ONE  
The curated gene families, called Reference Orthologous Groups, are publicly available at  ...  Herein, we used this dataset to demonstrate 1) why a manually curated, phylogeny-based dataset is more appropriate for benchmarking orthology than other popular practices and 2) how it guides database  ...  Acknowledgments The authors wish to thank all members of the Bork group for the fruitful discussions. Author Contributions Conceived and designed the experiments: PB.  ... 
doi:10.1371/journal.pone.0111122 pmid:25369365 pmcid:PMC4219706 fatcat:tfeqcwrnv5aaphnvskwafttf2u

Quantifying the mechanisms of domain gain in animal proteins

Marija Buljan, Adam Frankish, Alex Bateman
2010 Genome Biology  
By using animal gene phylogenies we were able to identify a set of high confidence domain gain events and by looking at their coding DNA investigate the causative mechanisms.  ...  Conclusions: The interplay of gene duplication and domain gain demonstrates an important mechanism for fast neofunctionalization of genes.  ...  , to M Babu, L Parts, M Taylor, S Pettit, A Elofsson and E Bornberg-Bauer for critical reading and comments on the manuscript and to P Coggill for proofreading of the manuscript.  ... 
doi:10.1186/gb-2010-11-7-r74 pmid:20633280 pmcid:PMC2926785 fatcat:viceqmmnc5g3nn5ykqfzdz4tki

PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools

Huaiyu Mi, Anushya Muruganujan, Dustin Ebert, Xiaosong Huang, Paul D Thomas
2018 Nucleic Acids Research  
For evolutionary classifications, we have added more prokaryotic and plant genomes to the phylogenetic gene trees, expanding the representation of gene evolution in these lineages.  ...  PANTHER (Protein Analysis Through Evolutionary Relationships, http://pantherdb.org) is a resource for the evolutionary and functional classification of genes from organisms across the tree of life.  ...  Briefly, curators review all experimental GO annotations for all genes in a family, in the context of the phylogenetic tree.  ... 
doi:10.1093/nar/gky1038 pmid:30407594 fatcat:cz662zk7yjhbrn2ph6l75ckdq4

Biological Databases for Human Research

Dong Zou, Lina Ma, Jun Yu, Zhang Zhang
2015 Genomics, Proteomics & Bioinformatics  
Here we present a collection of humanrelated biological databases and provide a mini-review by classifying them into different categories according to their data types.  ...  As human-related databases continue to grow not only in count but also in volume, challenges are ahead in big data storage, processing, exchange and curation.  ...  functional sites [83] SysPTM http://lifecenter.sgst.cn/SysPTM Post-translational modifications [84] TreeFam http://www.treefam.org Database of phylogenetic trees of animal species [24] UniPROBE  ... 
doi:10.1016/j.gpb.2015.01.006 pmid:25712261 pmcid:PMC4411498 fatcat:dubusegmv5gi5gcjxfrcaqhmvy

Functional Classification Using Phylogenomic Inference

Duncan Brown, Kimmen Sjölander
2006 PLoS Computational Biology  
Provides phylogenetic trees and orthology predictions for animal gene families.  ...  Propagates functional annotations across a tree topology using a noisy-or model of functional evolution. TREEFAM http://www.treefam.org Abbreviation for Tree Families Database.  ... 
doi:10.1371/journal.pcbi.0020077 pmid:16846248 pmcid:PMC1484587 fatcat:hsmwraxff5aijbzs4abcpadm3u

Aequatus: An open-source homology browser [article]

Anil S. Thanki, Nicola Soranzo, Javier Herrero, Wilfried Haerty, Robert P. Davey
2016 bioRxiv   pre-print
Phylogenetic information inferred from the study of homologous genes helps us to understand the evolution of genes and gene families, including the identification of ancestral gene duplication events as  ...  Findings: We present Aequatus, a standalone web-based tool that provides an in-depth view of gene structure across gene families, with various options to render and filter visualisations.  ...  Conflict of Interest: none declared.  ... 
doi:10.1101/055632 fatcat:kpdoqytjcvedrkajiyo3u2qrvu

Ancestral Genomes: a resource for reconstructed ancestral genes and genomes across the tree of life

Xiaosong Huang, Laurent-Philippe Albou, Tremayne Mushayahama, Anushya Muruganujan, Haiming Tang, Paul D Thomas
2018 Nucleic Acids Research  
The reconstructed genes are based on the extensive library of over 15 000 gene family trees from the PANTHER database, and are updated on a yearly basis.  ...  A growing number of whole genome sequencing projects, in combination with development of phylogenetic methods for reconstructing gene evolution, have provided us with a window into genomes that existed  ...  We chose to use a hierarchical, nested view of the species tree by default, rather than the phylogenetic tree view that is more traditional in phylogenetics.  ... 
doi:10.1093/nar/gky1009 pmid:30371900 pmcid:PMC6323951 fatcat:7fnve3dahjgt5gdxufdzfjbt4i

An Improved Indexing Method for Xpath Queries

Hoang Do Thanh Tung, Dinh Duc Luong
2016 Indian Journal of Science and Technology  
Our method is intended to apply to phylogenetic queries of Treefam databases.  ...  XPath is a method to quickly locate any information that we need in an XML (tree) data starting from the context node in a root node to subtrees.  ...  TreeFam (http://www. treefam.org) is a database of phylogenetic trees inferred from animal genomes, providing homology, orthology predictions together with the evolutionary history of the genes.  ... 
doi:10.17485/ijst/2016/v9i31/92731 fatcat:5f6uctzpb5a57a6ujwor6s4vni
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