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Murlet specifications


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


Alignment free comparative genomic screen for structured RNAs using coarse grained secondary structure dot plots

BMC Genomics
PMCID: 5712110
PMID: 29197323
DOI: 10.1186/s12864-017-4309-y

[…] e 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 from genomic […]


CompaRNA: a server for continuous benchmarking of automated methods for RNA secondary structure prediction

Nucleic Acids Res
PMCID: 3627593
PMID: 23435231
DOI: 10.1093/nar/gkt101

[…] ture in the context of the nature of their algorithms, i.e. whether a given method was trained on RNAs with known secondary structures. Examples of trained methods include ContextFold, ContraFold and Murlet. Methods that do not rely on the information about known RNA structures usually predict secondary structure based on free-energy minimization—examples include RNAfold and Sfold. The methods tha […]


Statistical evaluation of improvement in RNA secondary structure prediction

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 that is […]


PicXAA R: Efficient structural alignment of multiple RNA sequences using a greedy approach

BMC Bioinformatics
PMCID: 3044294
PMID: 21342569
DOI: 10.1186/1471-2105-12-S1-S38

[…] We use four different benchmark datasets: BRAliBase 2.1 [], Murlet [], BraliSub [], and LocalExtR [] to assess the performance of PicXAA-R on different alignment conditions. The first two are general datasets not specially designed for local RNA alignment test […]


MAGNOLIA: multiple alignment of protein–coding and structural RNA sequences

Nucleic Acids Res
PMCID: 2447753
PMID: 18515348
DOI: 10.1093/nar/gkn321

[…] with results for other alignment tools used in the benchmark. We also evaluated the accuracy of the secondary structure found by MAGNOLIA and compared it to two recent structural alignment programs: Murlet (16) and Mlocarna (17). For each software and for each identity class, we computed the percentage of correct base pairings amongst the set of predicted base pairings. Results are shown in . It […]


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

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

[…] 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. As for RNA […]


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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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