Evofold protocols

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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

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Source code is available upon request.

Publication for Evofold

Evofold in pipelines

 (4)
2011
PMCID: 3150283
PMID: 21829340
DOI: 10.1371/journal.pcbi.1002100

[…] searches is they have high false positive rates, around 50% . furthermore, a comparison of the encode regions that comprise one percent of the human genome show little overlap between rnaz, evofold, and cmfinder. even though the methods work in quite different ways, they all aim to fulfill the same task. this clearly shows that the area still needs to mature. a future direction […]

2011
PMCID: 3150283
PMID: 21829340
DOI: 10.1371/journal.pcbi.1002100

[…] initiated in this area ., compensating base pairs are clearly important, even though systematic analyses to study the impact have not been carried out. as discussed in , the overlap between rnaz, evofold, and cmfinder on the encode regions was poor, and a main difference was that a substantial amount of cmfinder candidates had more and more of the maf blocks re-aligned as sequence similarity […]

2007
PMCID: 1796608
PMID: 17288572
DOI: 10.1186/1471-2148-7-S1-S14

[…] are dedicated to search for mirnas [-] and programs such as rnaz, rnafold, mfold, ddbrna, randfold, msari, qrna, foldalign were written to detect stable rna secondary structures [,-]. a track (evofold) was also implemented into the ucsc genome browser, which indicates the potential of forming secondary structures for any give genomics locus. a number of databases have been created […]

2007
PMCID: 2072958
PMID: 17845718
DOI: 10.1186/1471-2164-8-316

[…] prediction of many thousands of genomic loci with evidence for stabilizing selection of rna structures [-]., despite the relatively high false positive rates of ncrna predictions by programs such as evofold, rnaz, and foldalign all these approaches yield clear statistical evidence that evolutionary conserved rna structure is a pervasive feature of eukaryotic genomes. the experimental […]


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Evofold in publications

 (60)
PMCID: 5712110
PMID: 29197323
DOI: 10.1186/s12864-017-4309-y

[…] 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 […]

PMCID: 5767953
PMID: 29149249
DOI: 10.1093/gbe/evx240

[…] ∼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 […]

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

[…] 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 […]

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

[…] computational methods to identify ncrnas; such as mfold [], rnafold [], and rnaz [], rely on formation of secondary structure, or combine this approach with comparative sequence analysis (such as evofold []). the formation of secondary structures is a feature of many ncrnas including; small nucleolar rnas, trnas, and micrornas; but many ncrnas and non-coding regulatory sequences […]

PMCID: 5473641
PMID: 28165450
DOI: 10.1038/ncomms14229

[…] of ashces and assembled transcripts from the chicken rna-seq data sets. to investigate potentially functional rna structures of ashces, we extracted the multiple alignments of each hce to run evofold v1.0 (ref. ) to identify functional rna structures (). we compared these rna structures to the chicken mirnas annotated in ensembl ()., to investigate whether the ashces harbour some lncrnas, […]


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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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