FOLDALIGN pipeline

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


Maintainer


  • person_outline FOLDALIGN <>

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


Documentation


Maintainer


  • person_outline FOLDALIGN <>

Publications for FOLDALIGN

FOLDALIGN IN pipelines

 (5)
2007
PMCID: 1868766
PMID: 17445273
DOI: 10.1186/1471-2105-8-130

[…] algorithm have been developed to find the secondary structure common to two sequences. each of these implementations restricts the search space to make the program runtime feasible. the first, foldalign [32], maximized an empirical score and originally did not allow multibranch loops to improve runtime. foldalign was later revised to allow multibranch loops and use a subset of the free […]

2007
PMCID: 1868766
PMID: 17445273
DOI: 10.1186/1471-2105-8-130

[…] restricts the search space to make the program runtime feasible. the first, foldalign [32], maximized an empirical score and originally did not allow multibranch loops to improve runtime. foldalign was later revised to allow multibranch loops and use a subset of the free energy nearest neighbor parameters [33]. the revised foldalign restricts the alignment space to reduce runtime. two […]

2007
PMCID: 1868766
PMID: 17445273
DOI: 10.1186/1471-2105-8-130

[…] did not allow multibranch loops to improve runtime. foldalign was later revised to allow multibranch loops and use a subset of the free energy nearest neighbor parameters [33]. the revised foldalign restricts the alignment space to reduce runtime. two scfg-based programs are available, stemloc package [11,12] and consan [34]. to reduce runtime, stemloc introduced the concept of fold […]

2007
PMCID: 1868766
PMID: 17445273
DOI: 10.1186/1471-2105-8-130

[…] co-incidence probabilities) and the previous dynalign banding constraint (m constraint) [35] were also compared against three other dynamic programming algorithms. the three other programs are foldalign [33], which uses a free energy-based scoring function, and stemloc [11] and consan [34], which use scfg models. each program was run using default parameters. our interest […]

2007
PMCID: 1950533
PMID: 17586815
DOI: 10.1093/nar/gkm474

[…] structural alignment was done using rsmatch1.0 converted for windows (original program is available at http://exon.umdnj.edu/software/rsmatch/) and foldalignm (http://foldalign.ku.dk/software/index.html).rrna sequence alignments for preliminary methylation site analysis were generated using clustalw (44)., rt-pcr reactions used invitrogen thermoscript first strand […]

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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