ArticleNature biotechnology2010
Comparative assessment of methods for aligning multiple genome sequences.
Article in Nature biotechnology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- FGCD: a database of fungal gene clusters related to secondary metabolism.Database : the journal of biological databases and curation · 2024Article
- Evolutionary insights into 3D genome organization and epigenetic landscape ofLife science alliance · 2024Article
- GALA: a computational framework for de novo chromosome-by-chromosome assembly with long reads.Nature communications · 2023Article
- GLAPD: Whole Genome Based LAMP Primer Design for a Set of Target Genomes.Frontiers in microbiology · 2019Article
- Systematic discovery of conservation states for single-nucleotide annotation of the human genome.Communications biology · 2019Article
- Inferring synteny between genome assemblies: a systematic evaluation.BMC bioinformatics · 2018Article
- Coordinate systems for supergenomes.Algorithms for molecular biology : AMB · 2018Article
- Evolution of Epigenetic Regulation in Vertebrate Genomes.Trends in genetics : TIG · 2016Review
- Ensembl comparative genomics resources.Database : the journal of biological databases and curation · 2016Article
- Identification and computational analysis of gene regulatory elements.Cold Spring Harbor protocols · 2015Review
- Alignathon: a competitive assessment of whole-genome alignment methods.Genome research · 2014Article
- Metabolic network motifs can provide novel insights into evolution: The evolutionary origin of Eukaryotic organelles as a case study.Computational biology and chemistry · 2014Article
- GenomeVISTA--an integrated software package for whole-genome alignment and visualization.Bioinformatics (Oxford, England) · 2014Article
- Tracing the evolution of lineage-specific transcription factor binding sites in a birth-death framework.PLoS computational biology · 2014Article
- Testing robustness of relative complexity measure method constructing robust phylogenetic trees for Galanthus L. using the relative complexity measure.BMC bioinformatics · 2013Article
- Thermally assisted quantum annealing of a 16-qubit problem.Nature communications · 2013Article
- Changes in exon-intron structure during vertebrate evolution affect the splicing pattern of exons.Genome research · 2012Article
- Rigorous and thorough bioinformatic analyses of olfactory receptor promoters confirm enrichment of O/E and homeodomain binding sites but reveal no new common motifs.BMC genomics · 2011Article
- Identifying functional single nucleotide polymorphisms in the human CArGome.Physiological genomics · 2011Article
- Exploring the selective constraint on the sizes of insertions and deletions in 5' untranslated regions in mammals.BMC evolutionary biology · 2011Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Multiple sequence alignment is a difficult computational problem. There have been compelling pleas for methods to assess whole-genome multiple sequence alignments and compare the alignments produced by different tools. We assess the four ENCODE alignments, each of which aligns 28 vertebrates on 554 Mbp of total input sequence. We measure the level of agreement among the alignments and compare their coverage and accuracy. We find a disturbing lack of agreement among the alignments not only in species distant from human, but even in mouse, a well-studied model organism. Overall, the assessment shows that Pecan produces the most accurate or nearly most accurate alignment in all species and genomic location categories, while still providing coverage comparable to or better than that of the other alignments in the placental mammals. Our assessment reveals that constructing accurate whole-genome multiple sequence alignments remains a significant challenge, particularly for noncoding regions and distantly related species.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.