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Murlet specifications

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Unique identifier OMICS_03475
Name Murlet
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability No
Maintained No

Publication for Murlet

Murlet citations

 (4)
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

[…] 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 to perform an all-against-all scan of all windows […]

library_books

Statistical evaluation of improvement in RNA secondary structure prediction

2011
Nucleic Acids Res
PMCID: 3287165
PMID: 22139940
DOI: 10.1093/nar/gkr1081

[…] benchmark results published previously (). this benchmark consists of 400 trna sequences () predicted by 12 methods, namely, fold (), dynalign (), multilign (), foldalignm (), mlocarna (), mastr (), murlet (), raf (), rnasampler (), rnashapes (), stemloc () and rnaalifold (). fold finds the lowest free energy structure for a single sequence. dynalign finds the lowest free energy structure […]

library_books

Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT based framework

2008
BMC Bioinformatics
PMCID: 2387179
PMID: 18439255
DOI: 10.1186/1471-2105-9-212

[…] a 3.6 ghz intel xeon with 4 gb of ram., there are presently about a dozen methods for global multiple ncrna alignment. as representatives of the exiting methods, we selected the five latest methods, murlet [], mxscarna [], rna sampler [], lara [] and mastr [], which reportedly outperformed the other methods, including foldalignm [], rnacast [], dynalign [] and stemloc [], consistently. […]

library_books

A fast structural multiple alignment method for long RNA sequences

2008
BMC Bioinformatics
PMCID: 2375124
PMID: 18215258
DOI: 10.1186/1471-2105-9-33

[…] alignment as an integer linear program (ilp), and implemented it in rnalara []. kiryu et al. proposed a variant of sankoff's algorithm with marked reduction of computation, which was implemented in murlet []. all of these methods, however, are still too slow to apply to the rna sequences longer than 1000 bases. seibel et al. developed an alignment tool with an editor, which uses the secondary […]


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Murlet institution(s)
Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, Koto-ku, Tokyo, Japan

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