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Enredo specifications

Information


Unique identifier OMICS_24704
Name Enredo
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data A set of complete (or near complete) genomes and a set of nonoverlapping GPAs.
Operating system Unix/Linux
Computer skills Advanced
Maintained No

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Publication for Enredo

Enredo citations

 (42)
library_books

Large scale variation in the rate of germ line de novo mutation, base composition, divergence and diversity in humans

2018
PLoS Genet
PMCID: 5891062
PMID: 29590096
DOI: 10.1371/journal.pgen.1007254

[…] http://hgdownload.cse.ucsc.edu/goldenpath/hg19/vsPanTro4/) (ii) the UCSC MultiZ (MZ) 46-way alignments [] downloaded from http://hgdownload.cse.ucsc.edu/goldenpath/hg19/multiz46way/ and (iii) Ensembl Enredo, Pecan, Ortheus (EPO) 6 primate multiple alignment, release 74, [] downloaded from ftp://ftp.ensembl.org/pub/release-74/emf/ensembl-compara/epo_6_primate/. We found that the EPO alignments were […]

library_books

Functional analysis of a novel, thyroglobulin embedded microRNA gene deregulated in papillary thyroid carcinoma

2017
Sci Rep
PMCID: 5577171
PMID: 28855631
DOI: 10.1038/s41598-017-10318-w

[…] ve pre-miRNA hairpin meets the criteria of minimum free energy (MFE) ≤ −30 kcal/ml and the shape probability ≥ 70%. The analysis of evolutionary conservation of sequence was performed with the use of Enredo, Pecan, Ortheus (EPO) tools available on Ensembl Genome Browser.TargetRank was used to predict target genes for the novel miR-TG. Only genes with both increased expression in thyroid tumors and […]

library_books

Identification of candidate protective variants for common diseases and evaluation of their protective potential

2017
BMC Genomics
PMCID: 5543444
PMID: 28774272
DOI: 10.1186/s12864-017-3964-3

[…] on was inferred from whole genome alignments of 6 primate species (H. sapiens, P. troglodytes, G. gorilla, P. pygmaeus, M. mulatta and C. jacchus) released in Ensembl Compara 59 which implemented the Enredo-Pecan-Ortheus (EPO) alignment method []. We accessed this information from phase 1 of the 1000 Genomes project [] by applying the tabix command from the SAM tools package [] to the relevant chr […]

library_books

High precision detection of conserved segments from synteny blocks

2017
PLoS One
PMCID: 5495381
PMID: 28671949
DOI: 10.1371/journal.pone.0180198

[…] ,,] that may be more difficult to configure []. In addition, it has been demonstrated [] that structures of such graphs “do not show crucial pieces of alignment information”. For instance, except for Enredo[], they do not display mono-genic inversions.Here, we considered chromosomes as linear arrays of ordered and oriented genes, but considering nucleotide sequences could help resolve some remaini […]

library_books

Genetic loci associated with coronary artery disease harbor evidence of selection and antagonistic pleiotropy

2017
PLoS Genet
PMCID: 5480811
PMID: 28640878
DOI: 10.1371/journal.pgen.1006328

[…] ted to ancestral and derived states using python script. Ancestral allele states came from 1000 Genomes Project FASTA files and derived 6-primate (human, gorilla, orangutan, chimp, macaque, marmoset) Enredo-Pecan-Ortheus alignment [] from the Ensembl Compara 59 database []. […]

library_books

Imbalance Aware Machine Learning for Predicting Rare and Common Disease Associated Non Coding Variants

2017
Sci Rep
PMCID: 5462751
PMID: 28592878
DOI: 10.1038/s41598-017-03011-5

[…] leotides were identified in the human reference genome sequence (hg19) differing, in high confidence alignment regions, from the ancestral primate genome sequence inferred on the basis of the Ensembl Enredo-Pechan-Ortheus (EPO) whole-genome alignments of six primate species, (Ensembl Compara release e71). In order to filter out variants that had not been exposed to many generations of natural sel […]

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Enredo institution(s)
Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA, USA; EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK

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