FOLDALIGN protocols

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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

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Documentation


Publications for FOLDALIGN

FOLDALIGN in pipelines

 (9)
2016
PMCID: 5444242
PMID: 26984616
DOI: 10.1093/bib/bbw022

[…] alignment to derive the final sequence alignment from it. aside from better speed, we hoped for a performance improvement in the dent zone. testing the new approach, it perfectly fell between foldalign [] and pmcomp [], exactly reproducing the dent in the twilight area. this was puzzling, as the approach is quite different in nature from the sankoff-type approaches. we believed that human […]

2013
PMCID: 3691524
PMID: 23621982
DOI: 10.1186/1471-2105-14-142

[…] fold structure simultaneously. excessive computational resources (o(n6)) are required by the sankoff algorithm for a large-scale problem. some implementations of this approach, such as dynalign [], foldalign [], locarna [] and conan [], attempt to restrict its solution space by limiting the number of possible sub-structures. however these methods are still computationally expensive (o(n4))., […]

2009
PMCID: 2709569
PMID: 19429694
DOI: 10.1093/nar/gkp276

[…] (). the dataset is the same dataset that was utilized in benchmarking experiments performed in a previous paper (), so results are directly comparable with previous benchmarks on dynalign (), foldalign (), stemloc (), consan (), locarna () and single sequence structure prediction based on free energy minimization (). the cluster analysis was performed on the generated sample of structures […]

2008
PMCID: 2630964
PMID: 19061486
DOI: 10.1186/1471-2105-9-521

[…] alignment methods. the programs and command line options are summarized in table . to perform the comparisons on an equal footing, global alignment mode was used for local alignment programs, foldalign and locarna., in this table, 'program' and 'version' columns indicate program names and their versions, respectively. in 'command' column, executable file names and options we used […]

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

[…] real homologs from negative controls., programs such as mirscan, mirseeker and promir 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 […]


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FOLDALIGN in publications

 (36)
PMCID: 5712110
PMID: 29197323
DOI: 10.1186/s12864-017-4309-y

[…] computational cost in terms of run-time and memory usage for any practical use. to circumvent this problem, restricted, approximated or alternative versions of the sankoff-style algorithm, including foldalign [–], dynalign [–], cmfinder [], locarna [, ], murlet [], raf [] and dafs [], have been published with/without application to ncrna discovery. however, these methods are still too slow […]

PMCID: 5727460
PMID: 29069516
DOI: 10.1093/nar/gkx979

[…] that has broad physiological significance., 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 […]

PMCID: 5259865
PMID: 28155712
DOI: 10.1186/s12864-016-3325-7

[…] 4.6.1) [] with cutoff fdr of 0.05.ii) secondary structure motif prediction. (1) to identify “seeds” of secondary structure motifs, pairwise alignment considering secondary structure was performed by foldalign software (version 2.5) [] over the sets of bins of a cluster of interest. (2) from the identified alignments with various lengths and alignment scores, we chose the “seeds” according […]

PMCID: 5444242
PMID: 26984616
DOI: 10.1093/bib/bbw022

[…] b-type algorithms as of 2005 perform better. with decreasing sequence identity, their performance degrades more gracefully overall. shows the effect of smoothing on two of the curves. the green (foldalign), purple (pmcomp) and brown (dynalign) curves represent the three best performing plan b approaches. to a varying degree, they show a decline in the area between 60–40% identity, whereas […]

PMCID: 4468099
PMID: 26075601
DOI: 10.1371/journal.pone.0130200

[…] cmfinder [] searches for common structures among unaligned sequences by comparing local structures predicted on single sequences. another approach is taken by methods based on dynalign [, ] and foldalign [], which use algorithms that fold and align two sequences simultaneously. the structural alignment quality is therefore not adversely affected by low sequence similarity […]


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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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