CMfinder protocols

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CMfinder specifications

Information


Unique identifier OMICS_03472
Name CMfinder
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 0.2
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Zizhen Yao <>

Information


Unique identifier OMICS_03472
Name CMfinder
Interface Web user interface
Restrictions to use None
Computer skills Basic
Version 0.2
Stability Stable
Maintained Yes

Maintainer


  • person_outline Zizhen Yao <>

Publication for CMfinder

CMfinder in pipelines

 (6)
2013
PMCID: 3760282
PMID: 24002378
DOI: 10.1038/srep02468

[…] sequence. shows the structural alignment produced using stral and petfold via the war web server. the central part of the conserved hairpin structure is also supported by mastr, locarna, mxcarna, cmfinder and petfold (http://genome.ku.dk/resources/war/). using the sequenced genome of hpiv4_dk(459) we later designed a simple diagnostic real-time pcr assay (see material and methods and ) […]

2013
PMCID: 3765725
PMID: 23947565
DOI: 10.1186/1471-2164-14-558

[…] integrated genomics viewer []., homologous srnas were identified using blastn (e-value less than 1e-06) and aligned using clustal omega [,]. selected alignments were computationally folded using cmfinder [] on the war webserver []. compensatory mutations that maintained secondary structure were located manually and the varna software package [] was used to illustrate rna secondary structure. […]

2012
PMCID: 3384581
PMID: 22336713
DOI: 10.4161/rna.19160

[…] apis mellifera, tribolium castaneum, capitella teleta, daphnia pulex, caenorhabditis elegans, gallus gallus, mus musculus and homo sapiens. we aligned the putative microrna hairpin sequences with cmfinder (n = 5, m = 30, m = 100), chose the output alignment that best reflects the microrna hairpin pairing, and manually refined the alignment using ralee. the consensus sequence of the alignment […]

2011
PMCID: 3150283
PMID: 21829340
DOI: 10.1371/journal.pcbi.1002100

[…] is they have high false positive rates, around 50% . furthermore, a comparison of the encode regions that comprise one percent of the human genome show little overlap between rnaz, evofold, and cmfinder. even though the methods work in quite different ways, they all aim to fulfill the same task. this clearly shows that the area still needs to mature. a future direction is to improve […]

2011
PMCID: 3150283
PMID: 21829340
DOI: 10.1371/journal.pcbi.1002100

[…] in this area ., compensating base pairs are clearly important, even though systematic analyses to study the impact have not been carried out. as discussed in , the overlap between rnaz, evofold, and cmfinder on the encode regions was poor, and a main difference was that a substantial amount of cmfinder candidates had more and more of the maf blocks re-aligned as sequence similarity dropped, […]


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CMfinder in publications

 (55)
PMCID: 5770649
PMID: 29375488
DOI: 10.3389/fmicb.2017.02432

[…] species, none have been experimentally confirmed in z. mobilis. three riboswitches (two cobalamine and one tpp riboswitches) have been predicted in z. mobilis genome by computational analysis using cmfinder, suggesting that these regulatory elements are likely present in this organism (yao et al., ). in this work, available transcriptomic data were searched with a bioinformatics approach […]

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

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

PMCID: 5705152
PMID: 29182646
DOI: 10.1371/journal.pone.0188441

[…] defined as the 450 bp downstream of the stop codon for the 3’-utrs, and the 150 bp upstream and 50 bp downstream of the aug codon for the 5’-utrs. for the discovery of the motifs, the algorithm cmfinder [] was used with the following parameters: “−s1 −f 0.4−c10”. a further assessment of the quality of the identified motif was sought by calculating a sensitivity and specificity value. […]

PMCID: 5694010
PMID: 29150605
DOI: 10.1038/s41467-017-01613-1

[…] and the significantly enriched clip-seq peaks was 136 bases., zagros was used to identify enriched sequence motifs in the clip-seq peaks using both secondary structure and sequence information. cmfinder was used with default settings to identify the top enriched structural motif. to compare the frequency of the auggaug in the clip-seq peaks to the e. coli genome, fimo (find individual motif […]

PMCID: 5640933
PMID: 29029611
DOI: 10.1186/s12864-017-4171-y

[…] that are only poorly conserved at the nucleotide level []. as a result, some successful computational search strategies for structured ncrna candidates use algorithms such as qrna [], rnaz [], or cmfinder [], which search for nucleotide covariation or other evidence of structure formation and conservation, rather than just searching for conserved sequence. a computational search across […]


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CMfinder institution(s)
Department of Computer Science and Engineering, University of Washington Seattle, USA

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