PEMer statistics

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Citations per year

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Popular tool citations

chevron_left Deletion detection Insertion detection Structural variant detection Inversion detection chevron_right
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Associated diseases

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PEMer specifications

Information


Unique identifier OMICS_00320
Name PEMer
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input format FASTA
Operating system Unix/Linux
Programming languages Perl, Python
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for PEMer

PEMer in publications

 (7)
PMCID: 5852634
PMID: 29623115
DOI: 10.3762/bjoc.14.40

[…] electrocatalytic hydrogenation of benzophenone was performed at room temperature and atmospheric pressure using a polymer electrolyte membrane electrochemical reactor (pemer). palladium (pd) nanoparticles were synthesised and supported on a carbonaceous matrix (pd/c) with a 28 wt % of pd with respect to carbon material. pd/c was characterised by transmission […]

PMCID: 4827795
PMID: 27081306
DOI: 10.4137/CIN.S30793

[…] mapped paired reads generated in a discordant manner, whose distances differ very significantly from a predefined or a usual average distance of paired reads. therefore, pem-based methods such as pemer and breakdancer can efficiently detect many kinds of svs including insertions, deletions, inversions, and tandem duplication, but are not capable of detecting svs in low-resolution […]

PMCID: 4545535
PMID: 26286629
DOI: 10.1186/s40246-015-0042-2

[…] read mapping methods compare the expected distance to the actual mapped distance to determine whether there is any indel in the sequence (fig.  ()). tools belonging to this category include pemer [], hydra [], and breakdancer []. haplotype-based methods first identify the regions of interest where the reads show substantial evidence of having indels relative to the reference sequence. […]

PMCID: 4479793
PMID: 26161383
DOI: 10.3389/fbioe.2015.00092

[…] larger than the average insert size. several tools based on the detection of sv signatures from clusters of read-pairs have been reported in the literature including breakdancer, variationhunter, pemer, and gasv (chen et al., ; hormozdiari et al., , ; korbel et al., ; sindi et al., ). remarkably, pemer can be exploited for the identification of linked insertions (medvedev et al., )., clusters […]

PMCID: 4475638
PMID: 25985233
DOI: 10.1038/ni.3160

[…] resulting files were analyzed using genespring (agilent). the mate status was fixed to exclude reads with an inconsistent mate status. a minimum indel detection size of 100 bp was applied using the pemer indel detection algorithm. the minimum local deviant read coverage used was 11 and the minimum local deviant read fraction was 0.2., data are presented as the mean ± s.d. the comparisons […]


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PEMer institution(s)
Gene Expression Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstr, Heidelberg, Germany

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