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Protocols

HOVERGEN specifications

Information


Unique identifier OMICS_05352
Name HOVERGEN
Restrictions to use None
Maintained Yes

Maintainer


  • person_outline Laurent Duret

Publication for HOVERGEN

HOVERGEN citations

 (7)
library_books

An improved alignment free model for dna sequence similarity metric

2014
BMC Bioinformatics
PMCID: 4261891
PMID: 25261973
DOI: 10.1186/1471-2105-15-321

[…] sed k-means with UCLUST and CD-HIT, which are two alignment based DNA clustering models.Seven datasets DS2, DS3, DS4, HOG20, HOG50, HOG80 and HOG100 are collected from PBIL []. The DS2 dataset is the HOVERGEN from PBIL, which is a database of homologous vertebrate genes. The DS4 is randomly selected from HOMOLENS, which is a database of homologous genes from Ensembl organisms and Ensembl families. […]

library_books

Conceptual framework and pilot study to benchmark phylogenomic databases based on reference gene trees

2011
Brief Bioinform
PMCID: 3178055
PMID: 21737420
DOI: 10.1093/bib/bbr034

[…] ene duplication at each internal node. Hence, all possible orthologous and paralogous gene relationships can be directly derived from a resolved tree. Annotated gene trees are constructed by Compara, HOVERGEN and Panther; plain gene trees by HOGENOM. eggNOG and InParanoid also provide gene trees but they are not used to infer orthology.Thus, concepts differ in the extent to which they capture phyl […]

call_split

The two tryptophans of β2 microglobulin have distinct roles in function and folding and might represent two independent responses to evolutionary pressure

2011
BMC Evol Biol
PMCID: 3124429
PMID: 21663612
DOI: 10.1186/1471-2148-11-159
call_split See protocol

[…] We used the FamFetch tool with the entry name B2MG_HUMAN to search the HOVERGEN database. The retrieved family, HBG006197, consisted of 130 protein sequences from 96 different species with Gnathostomata as a common ancestor. We selected a single sequence for each species […]

library_books

Transcriptome analysis in non model species: a new method for the analysis of heterologous hybridization on microarrays

2010
BMC Genomics
PMCID: 2901317
PMID: 20509979
DOI: 10.1186/1471-2164-11-344

[…] For this purpose, we used all Aptenodytes patagonicus mRNA sequences available in GenBank. For each of these sequences, we identified the most similar gene family in the Hovergen homologous gene families database []. We then replaced the penguin sequence in the phylogenetic tree of the family, which allowed us to identify the putatively orthologous chicken sequence, i […]

library_books

The 20th anniversary of EMBnet: 20 years of bioinformatics for the Life Sciences community

2009
BMC Bioinformatics
PMCID: 2697632
PMID: 19534734
DOI: 10.1186/1471-2105-10-S6-S1

[…] massive all-against-all similarity searches, gene clustering, multiple alignments computation, and phylogenetic tree reconstruction and reconciliation which led to the production of three databases: HOVERGEN, HOGENOM and HOMOLENS.Other example of new tools are represented by the work of Sperber et al. [], who created 'RetroTector' for the study of retroviral elements in vertebrates; by the work o […]

library_books

Developmental Constraints on Vertebrate Genome Evolution

2008
PLoS Genet
PMCID: 2600815
PMID: 19096706
DOI: 10.1371/journal.pgen.1000311

[…] Gene families were obtained from the HomolEns database version 3 (http://pbil.univ-lyon1.fr/databases/homolens.html), which is based on Ensembl release 41 . HomolEns is build on the same model as Hovergen , with genes organized in families, which include pre-calculated alignments and phylogenies. In HomolEns version 3, alignments are computed with MUSCLE (with default parameters), and phyloge […]

Citations

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HOVERGEN institution(s)
Laboratoire de Biométrie et Biologie Evolutive, CNRS, Université Claude Bernard - Lyon 1, Villeurbanne, France

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