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HOMOLENS specifications

Information


Unique identifier OMICS_05351
Name HOMOLENS
Restrictions to use None
Maintained Yes

Publication for HOMOLENS

HOMOLENS citations

 (6)
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

[…] , 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. The rest are randomly selected from HOGENOM, which contains homologous gene families from microbial organ […]

library_books

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

[…] similarity search against current databases, performed using the Blast algorithm. A more accurate approach is based on the databases of homologous genes, which are available as HOVERGEN, HOGENOM and HOMOLENS [-].A BLASTP search of our protein of interest (human β2-m) against the NCBInr database allowed us to retrieve homologous sequences only from vertebrates. As a consequence we decided to consi […]

library_books

An efficient method to find potentially universal population genetic markers, applied to metazoans

2010
BMC Evol Biol
PMCID: 2949868
PMID: 20836842
DOI: 10.1186/1471-2148-10-276

[…] The Famfetch software [] was used to query revision 2 (stage I of our search) or revision 3 (stages II and III) of the Homolens database of homologous gene families [] from Ensembl, and retain families for which orthologs were found in Homo, Rodentia, Canis, Gallus, Danio, Xenopus, Percomorpha, Ciona, Insecta, and Nem […]

library_books

Large Scale Analysis of Orthologs and Paralogs under Covarion Like and Constant but Different Models of Amino Acid Evolution

2010
Mol Biol Evol
PMCID: 2955734
PMID: 20551039
DOI: 10.1093/molbev/msq149

[…] We used gene sequences and trees from the database HomolEns release 4 (), which is based on Ensembl release 49 (March 2008; ) March 2008 being the date of release 49. Genes are organized in families, which include precalculated alignments and phylogen […]

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

[…] ll 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 of Rubino and Attimonel […]

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 famili […]

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

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