ArticleBMC bioinformatics2007
How accurately is ncRNA aligned within whole-genome multiple alignments?
Article in BMC bioinformatics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Uncovering deeply conserved motif combinations in rapidly evolving noncoding sequences.Genome biology · 2021Article
- Article
- Split-inducing indels in phylogenomic analysis.Algorithms for molecular biology : AMB · 2018Article
- The identification and functional annotation of RNA structures conserved in vertebrates.Genome research · 2017Article
- Structured RNAs and synteny regions in the pig genome.BMC genomics · 2014Article
- Widespread purifying selection on RNA structure in mammals.Nucleic acids research · 2013Article
- Structure-based whole-genome realignment reveals many novel noncoding RNAs.Genome research · 2013Article
- From structure prediction to genomic screens for novel non-coding RNAs.PLoS computational biology · 2011Review
- Improved measurements of RNA structure conservation with generalized centroid estimators.Frontiers in genetics · 2011Article
- Robust and accurate prediction of noncoding RNAs from aligned sequences.BMC bioinformatics · 2010Article
- Rapid evolution of mammalian X-linked testis microRNAs.BMC genomics · 2009Article
- Local conservation scores without a priori assumptions on neutral substitution rates.BMC bioinformatics · 2008Article
- Comparative genomics beyond sequence-based alignments: RNA structures in the ENCODE regions.Genome research · 2008Article
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3 authors.
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Abstract
backgroundMultiple alignment of homologous DNA sequences is of great interest to biologists since it provides a window into evolutionary processes. At present, the accuracy of whole-genome multiple alignments, particularly in noncoding regions, has not been thoroughly evaluated.
resultsWe evaluate the alignment accuracy of certain noncoding regions using noncoding RNA alignments from Rfam as a reference. We inspect the MULTIZ 17-vertebrate alignment from the UCSC Genome Browser for all the human sequences in the Rfam seed alignments. In particular, we find 638 instances of chimeric and partial alignments to human noncoding RNA elements, of which at least 225 can be improved by straightforward means. As a byproduct of our procedure, we predict many novel instances of known ncRNA families that are suggested by the alignment.
conclusionMULTIZ does a fairly accurate job of aligning these genomes in these difficult regions. However, our experiments indicate that better alignments exist in some regions.
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