CMsearch protocols

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CMsearch specifications

Information


Unique identifier OMICS_13452
Name CMsearch
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python
Computer skills Advanced
Stability Stable
Maintained Yes

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  • person_outline Xin Gao <>

Publication for CMsearch

CMsearch in pipelines

 (10)
2018
PMCID: 5880011
PMID: 29606099
DOI: 10.1186/s12862-018-1161-x

[…] u2 (rf00004), u4 (rf00015), u5 (rf00020) and u6 (rf00026) from the rfam database []. the alignments were calibrated (using cmcalibrate) and then used for snrna searches in red algal genomes (using cmsearch) using infernal (v1.1.2) with the default settings []., we downloaded the genome and coding dna sequences (cdss) from six red algal species that have high-quality whole genome sequences: g. […]

2017
PMCID: 5522923
PMID: 28729256
DOI: 10.1128/genomeA.00496-17

[…] of 647×. the complete genome was analyzed by genemarks () for gene prediction, trnascan-se () for trna, rrnammer () for rrna, and srna were predicted by blast against the rfam database () and cmsearch (version 1.1rc4). the interspersed repetitive sequences and tandem repeats were analyzed by repeatmasker () and trf (), respectively. as a result, the genome of zly1309f contains 1,208 […]

2016
PMCID: 4766624
PMID: 26911872
DOI: 10.1186/s13059-016-0883-6

[…] to the 12 plant genomes using all bean transcript models as templates. lncrna transcript expressions were obtained using the flux capacitor []., small non-coding rnas were predicted using the cmsearch tool from the infernal package (v.1.1rc2) []. an e-value cutoff of 0.01 allowed detection of 2529 non-overlapping hits; of these, 258 are in contigs and 2271 in scaffolds. we were able […]

2016
PMCID: 4770515
PMID: 26923790
DOI: 10.1186/s12864-016-2474-z

[…] in k. marxianus genome, we predicted protein coding genes by using augustus with default parameters and trained with gene set of k. lactis []. for rna gene annotation, we predicted genes using cmsearch of infernal (1.1rc4) and rfam (version 12.0) [, ]. we discarded manually apparent non-yeast entries, such as bacteria, originating after discarding entries with p-value over 0.01. gene name […]

2016
PMCID: 5034121
PMID: 27660770
DOI: 10.1128/genomeA.00930-16

[…] genes encoding trnas were determined using the trnascan-se () and structural rnas (5s, 16s, and 23s rrnas) were used in a blastn search against the reference set. 5s hits were further refined using cmsearch. functional annotation was achieved using the web cd search tool () and blast against the ardb (antibiotic resistance genes database) ()., the genome from k. pneumoniae strain […]


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CMsearch in publications

 (77)
PMCID: 5915480
PMID: 29720997
DOI: 10.3389/fgene.2018.00130

[…] utility provided with augustus and position hints from ptr pt-1c-bfp proteins (assembly asm14998v1) mapped to each genome using exonerate v2.2.0 (). non-coding rna genes were identified using cmsearch () using the non-coding rnas distributed with the companion annotation workflow ()., a rough distance matrix was constructed to inform the whole genome alignment. minhash distance estimation […]

PMCID: 5913331
PMID: 29719549
DOI: 10.3389/fgene.2018.00124

[…] filtering and a graph-based clustering method that utilizes rna secondary structure information. we tested the specificity, sensitivity and runtime of glassgo, blast and the combination rnalien/cmsearch in a typical use case scenario on 40 bacterial srna families. the sensitivity of the tested methods was similar, while the specificity of glassgo and rnalien/cmsearch was significantly […]

PMCID: 5882874
PMID: 29615754
DOI: 10.1038/s41598-018-23900-7

[…] for the recognition of pyrimidine and pyrophosphate and are found to be highly conserved across the phylogeny. we used the rfam seed alignment (based on the covariance model) of tpp and the cmsearch application to search against a database consisting of the ten reference sequences mentioned above and generated separate sequence alignments of the tpp aptamers regulating thi4, nmt1 […]

PMCID: 5880011
PMID: 29606099
DOI: 10.1186/s12862-018-1161-x

[…] u2 (rf00004), u4 (rf00015), u5 (rf00020) and u6 (rf00026) from the rfam database []. the alignments were calibrated (using cmcalibrate) and then used for snrna searches in red algal genomes (using cmsearch) using infernal (v1.1.2) with the default settings []., we downloaded the genome and coding dna sequences (cdss) from six red algal species that have high-quality whole genome sequences: g. […]

PMCID: 5828423
PMID: 29482646
DOI: 10.1186/s40168-018-0420-9

[…] determined using two approaches: first, we counted the number of annotated 16s rrna sequences in the ncbi annotations (files rna_from_genomic.fna). second, we used covariance models with the program cmsearch (as part of infernal version 1.1.2, options “--noali --cut_nc”) to search for 16s rrna sequences within the assembled genomes (files genomic.fna). separate covariance models for archaeal […]


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CMsearch institution(s)
King Abdullah University of Science and Technology, Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering, Division, Thuwal, Saudi Arabia; Beijing Key Laboratory of Big Data Management and Analysis Methods, School of Information, Renmin University of China, Beijing, China; Toyota Technological Institute at Chicago, Chicago, IL, USA; Department of Human Genetics, University of Chicago, Chicago, IL, USA
CMsearch funding source(s)
The research reported in this publication was supported by the King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR) under Award No. URF/1/1976-04, National Natural Science Foundation of China, the Fundamental Research Funds for the Central Universities and the Research Funds of Renmin University of China (15XNLQ01), and IBM Global SUR Award Program.

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