Enredo and Pecan: genome-wide mammalian consistency-based multiple alignment with paralogs.

By Benedict Paten, Javier Herrero, Kathryn M Beal, Stephen Fitzgerald, Ewan Birney. Genome Research, 2008

344 citations recorded by the source corpus.

Pairwise whole-genome alignment involves the creation of a homology map, capable of performing a near complete transformation of one genome into another. For multiple genomes this problem is generalized to finding a set of consistent homology maps for converting each genome in the set of aligned genomes into any of the others. The problem can be divided into two principal stages. First, the partitioning of the input genomes into a set of colinear segments, a process which essentially deals with the complex processes of rearrangement. Second, the generation of a base pair level alignment map for each colinear segment. We have developed a new genome-wide segmentation program, Enredo, which produces colinear segments from extant genomes handling rearrangements, including duplications. We have then applied the new alignment program Pecan, which makes the consistency alignment methodology practical at a large scale, to create a new set of genome-wide mammalian alignments. We test both Enredo and Pecan using novel and existing assessment analyses that incorporate both real biological data and simulations, and show that both independently and in combination they outperform existing programs. Alignments from our pipeline are publicly available within the Ensembl genome browser.

Subfields: Genetics, Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/7623cb1450f7c578bd3d5d6061cbeedd845d9bdb

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Citations in the corpus

Ensembl 2015 (2014, background): “We continue to develop and expand our range of endpoints which now include EPO genomic alignments and gene gain/loss trees in JSON and PhyloXML formats, as well as query support for archived identifiers.”
A general framework for estimating the relative pathogenicity of human genetic variants (2014, methodology): “Mutation rate parameters as well as the size distribution of indels were estimated from six-way primate genome alignments 15 .”
progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement (2010, methodology): “7 is a new aligner that has been demonstrated to have excellent performance [33,45] by virtue of using probabilistic consistency during the anchoring process.”
Pol III binding in six mammalian genomes shows high conservation among amino acid isotypes, despite divergence in tRNA gene usage (2011, neutral): “To determine genomic conservation of tRNA loci, we used Ensembl’s PECAN multiple genome alignment of 16 amniotes, from Ensembl version 58, because it is the current best available (the only available) multiple species alignment which includes all the species described in this report 35 .”
Ensembl 2016 (2015, methodology): “The zebrafish assembly update resulted in recomputing 20 pairwise whole genome alignments and our fish Enredo Pecan Ortheus (EPO) multiple alignments (32).”
The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes (2014, background): “BSR [28], Magic [29], Mavid [30], Mauve [31-33], MGA [34], M-GCAT [35], Mugsy [36], TBA [37], multi-LAGAN [38], PECAN [39]), multiple genome alignment remains a challenging task due to the prevalence of horizontal gene transfer [26,40], recombination, homoplasy, gene conversion, mobile genetic eleme”
Computational pan-genomics: status, promises and challenges (2016, neutral): “graphs [100] and Cactus graphs [101, 102].”
A User's Guide to the Encyclopedia of DNA Elements (ENCODE) (2011, methodology): “Multiple alignments of the genomes of 33 mammalian species have been constructed by using the Enredo, Pecan, Ortheus approach (EPO) [99,100], and complementary multiple alignments are available through the UCSC browser (UCSC Lastz/ChainNet/ Multiz).”
Learning about human population history from ancient and modern genomes (2011, background): “Therefore, both the Neanderthal and Denisovan genomes were analysed by mapping them to human and chimpanzee genomes and to the in silico -reconstructed genome of the last common ancestor of chimpanzees and human”
ReMap 2018: an updated atlas of regulatory regions from an integrative analysis of DNA-binding ChIP-seq experiments (2017, methodology): “The computed GERP scores were obtained from the 24-way amniota vertebrates Pecan (15) multi-species alignment, and extracted from the Ensembl Compara database release v89 (16).”
Predicting variant deleteriousness in non-human species: applying the CADD approach in mouse (2018, methodology): “The mouse-rat ancestral genome is based on the EPO 17-eutherian-mammal alignments [25, 27, 28] (Additional file 1: Figure S2) provided by Ensembl release 83 [29].”