FOLDALIGN statistics

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Citations per year

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

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

FOLDALIGN specifications

Information


Unique identifier OMICS_08111
Name FOLDALIGN
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Two RNA sequences
Input format FASTA
Output data FOLDALIGN outputs the best local alignment score for each pair of positions in the two sequences. This list can be further processed to produce a list of non-overlapping local alignments between the two sequences.
Operating system Unix/Linux
Programming languages C++
Computer skills Advanced
Version 2.5.0
Stability Beta
Maintained Yes

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Documentation


Information


Unique identifier OMICS_08111
Name FOLDALIGN
Interface Web user interface
Restrictions to use None
Input data Two RNA sequences
Input format FASTA
Output data FOLDALIGN outputs the best local alignment score for each pair of positions in the two sequences. This list can be further processed to produce a list of non-overlapping local alignments between the two sequences.
Computer skills Basic
Version 2.5.0
Stability Stable
Maintained Yes

Download


download.png

Documentation


Publications for FOLDALIGN

FOLDALIGN citations

 (51)
call_split

DotAligner: identification and clustering of RNA structure motifs

2017
Genome Biol
PMCID: 5747123
PMID: 29284541
DOI: 10.1186/s13059-017-1371-3
call_split See protocol

[…] backtracking for T=0.25 (Additional file : Figure S2B). CARNA version 1.2.5 was run with parameters --write-structure --noLP --time-limit=120000. LocaRNA version 1.7.13 was run with parameter --noLP. FoldAlign version 2.1.1 was run with and without parameter -global. Default parameters were used for pmcomp, downloaded from https://www.tbi.univie.ac.at/RNA/PMcomp/, and RNApaln version 2.3.5. The cu […]

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

[…] DotcodeR with a step size of 10 and a very high sensitivity using the output of the current scan as input;Then use a structural alignment method optimized for finding local structural alignments like Foldalign [];Finally cluster the results with GraphClust [] or RNAscClust [] to find families of structures. A method like Structator [] could be used to search for missed members of the clusters. Rer […]

call_split

Conserved structures formed by heterogeneous RNA sequences drive silencing of an inflammation responsive post transcriptional operon

2017
Nucleic Acids Res
PMCID: 5727460
PMID: 29069516
DOI: 10.1093/nar/gkx979
call_split See protocol

[…] 3′ UTR sequences (500 nucleotides maximum) from candidate human and murine mRNAs were locally aligned pairwise with the human Cp GAIT element using the FOLDALIGN program (foldalign.ku.dk/server/index.html), which simultaneously folds and aligns two or more RNA sequences and can make structure predictions (–). The resulting hits were then folded using […]

library_books

Elucidating the Role of Host Long Non Coding RNA during Viral Infection: Challenges and Paths Forward

2017
PMCID: 5748604
PMID: 29053596
DOI: 10.3390/vaccines5040037

[…] one of several structures described by Nitsche et al. []. The most common methods for predicting the secondary and tertiary structure of lncRNA are extensively reviewed by Yan et al. []. Pfold [] and Foldalign [] are two examples of methods that use multiple sequence alignments to predict the RNA secondary structure. Mfold [] and RNAfold [] are popular examples of minimum free energy models. Alter […]

library_books

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

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

[…] present 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 (; ) to fly () to vertebrates (; , ).The output of each screen for conserved RNA sec […]

library_books

Non Coding RNAs in Lung Cancer: Contribution of Bioinformatics Analysis to the Development of Non Invasive Diagnostic Tools

2016
Genes
PMCID: 5295003
PMID: 28035947
DOI: 10.3390/genes8010008

[…] ,,]. A more effective approach represents the Sankoff algorithm which can simultaneously align and fold multiple sequences [,,,,]. Programs using the Sankoff algorithm are for instance RNAalifold [], FOLDALIGN [] and LocARNA [], in which a pairwise sequence alignment is generated and subsequently aligned and folded to calculate the optimal conserved secondary structure []. However, further extensi […]


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FOLDALIGN institution(s)
Center for non-coding RNA in Technology and Health, IKVH, University of Copenhagen, Denmark; Department of Computer Science, University of Brasilia, Brasília, Brazil

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