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Citations per year

Number of citations per year for the bioinformatics software tool Evofold
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Tool usage distribution map

This map represents all the scientific publications referring to Evofold per scientific context
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Protocols

Evofold specifications

Information


Unique identifier OMICS_18670
Name Evofold
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A multiple alignment and a phylogenetic tree.
Output data A specific RNA secondary-structure prediction and a folding potential score.
Operating system Unix/Linux
Computer skills Advanced
Stability No
Maintained No

Versioning


No version available

Maintainer


This tool is not available anymore.

Additional information


Source code is available upon request.

Publication for Evofold

Evofold citations

 (69)
library_books

Alignment free comparative genomic screen for structured RNAs using coarse grained secondary structure dot plots

2017
BMC Genomics
PMCID: 5712110
PMID: 29197323
DOI: 10.1186/s12864-017-4309-y

[…] lication to ncRNA discovery. However, these methods are still too slow to perform an all-against-all scan of all windows from genomic sequences.Examples of the align-then-fold algorithms are RNAz [], evofold [] and PETfold []. While these methods are fast and deliver accurate results, they also require that the input sequences have been aligned correctly. Because these methods rely on sequence ali […]

library_books

Functional annotation of structural ncRNAs within enhancer RNAs in the human genome: implications for human disease

2017
Sci Rep
PMCID: 5686184
PMID: 29138457
DOI: 10.1038/s41598-017-15822-7

[…] rs. The filtered files were scored with RNAz and REAPR on both strands with the default parameters. Predictions with final P-values higher than 0.5 were retrieved for the subsequent pipeline. For the EvoFold analysis, sequences with > 20% gaps relative to the human genome were first removed. Then, alignments with sequences from fewer than six species were eliminated. EvoFold was then applied to th […]

library_books

Human Accelerated Regions and Other Human Specific Sequence Variations in the Context of Evolution and Their Relevance for Brain Development

2017
Genome Biol Evol
PMCID: 5767953
PMID: 29149249
DOI: 10.1093/gbe/evx240

[…] occur ∼1 Ma. The conserved region was estimated to be 310–400 Myr old, because it is conserved down to the bird (chicken) ().Both genes form secondary RNA structures helix-loop-helix as determined by EvoFold (). ) studied the secondary structure of HAR1A in more detail, to reveal differences with the secondary structure in chimpanzee, which could explain different function in human, compared with […]

library_books

Dynamic hyper editing underlies temperature adaptation in Drosophila

2017
PLoS Genet
PMCID: 5550009
PMID: 28746393
DOI: 10.1371/journal.pgen.1006931

[…] y structure is present and was not detected by our aligning approach. Therefore, we determined the percentage of editing sites engaged in evolutionarily conserved secondary structures as predicted by EvoFold[]. Consistent with the data presented above, we observed that at 18°C editing sites were twice as likely to be present in regions of evolutionarily conserved secondary structure than were site […]

library_books

Genome wide identification of conserved intronic non coding sequences using a Bayesian segmentation approach

2017
BMC Genomics
PMCID: 5369223
PMID: 28347272
DOI: 10.1186/s12864-017-3645-2

[…] We analysed the pathway-focussed PFEs using the same methods used in the genome-wide analysis (EvoFold, RNAz, DNase I footprints, and fRNAdb entries). An example WIG profile of a 169 nt long PFE identified in the 3-way alignment of eya1 is shown in Fig. . Three possible translation phases (top) […]

library_books

RNAscClust: clustering RNA sequences using structure conservation and graph based motifs

2017
Bioinformatics
PMCID: 5870858
PMID: 28334186
DOI: 10.1093/bioinformatics/btx114

[…] this identity range sequence based alignments are no longer accurate enough to represent RNA structure conservation (; ). Examples of methods working on sequence based alignments include RNAz () and EvoFold (). Programs for structural alignment applied to genomic screens includes Foldalign, Dynalign, LocaRNA and CMfinder (; ; ; ). Corresponding screens for structure RNAs range from prokaryotes (; […]


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Evofold institution(s)
Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, CA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, PA, USA; Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, USA
Evofold funding source(s)
Supported by NHGRI (Grant 1P41HG02371) and the Danish Research Council (Grant 21–04–0444).

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