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HOMOLENS specifications


Unique identifier OMICS_05351
Restrictions to use None
Maintained Yes

Publication for HOMOLENS

HOMOLENS citations


An improved alignment free model for dna sequence similarity metric

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 […]


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

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 […]


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

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

[…] would save time. For stages II and III, CDS were retrieved and the corresponding nucleotide alignment was obtained using PAL2NAL, for each family. The first 58 protein alignments, taken by increasing Homolens (HBGxxxxxx) number, were examined visually, looking for introns that were present in all the deuterostome species of the alignment and that lay between regions conserved enough to design PCR […]


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

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 […]


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

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 […]


Developmental Constraints on Vertebrate Genome Evolution

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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