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PatMaN specifications

Information


Unique identifier OMICS_00997
Name PatMaN
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for PatMaN

PatMaN in pipelines

 (2)
2015
PMCID: 4765792
PMID: 26357884
DOI: 10.1093/jxb/erv420

[…] expression levels of mirnas were measured by the small rna abundance. the amount of small rna reads was transformed into reads per million (rpm) with the formula rpm=reads count/clean reads×106). patman was employed to map the small rna reads to mature mirna sequences. small rna reads were counted when their position was within the length of the mature mirna sequence. the mirna read […]

2015
PMCID: 4765792
PMID: 26357884
DOI: 10.1093/jxb/erv420

[…] the function ‘user-submitted small rnas/ user-submitted transcripts’, the query of transcripts was generated from the b. napus genome. default parameters were used to filter candidates. the software patman was used to map the degradomic reads to the targets, and custom perl scripts were employed to identify candidate degradative targets. according to previous results (; ; ; ), the ends […]


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PatMaN in publications

 (57)
PMCID: 5825024
PMID: 29474379
DOI: 10.1371/journal.pone.0191966

[…] class distributions []., in non-redundant format, the reads were mapped to the reference genome (d. melanogaster v 6.11) and associated annotations, allowing 0, 1 or 2 mis-matches and 0 gaps using patman [,]. the reads were also mapped to mature mirnas and mirna hairpins, retrieved from mirbase, release 21 []. the srna analysis was conducted using the uea srna workbench, custom-made perl and r […]

PMCID: 5826055
PMID: 29516005
DOI: 10.3389/fsurg.2018.00007

[…] non-invasive means of obtaining rapid vascular control in the exsanguinating abdominal trauma patient ()., injury of the ca is rare and may occur at the main trunk or any of its branches (). since patman et al. () reported the first case, few studies (–) are available in the literature (table ). asensio et al. () presented the largest series in the literature, in which 12 patients suffered […]

PMCID: 5774138
PMID: 29347911
DOI: 10.1186/s12864-018-4436-0

[…] ends) of the reads were also trimmed []. reads consisting 16–35 nt were kept for further analysis. srnas were mapped full length with no gaps or mismatches allowed to the x. laevis genome (v8) using patman []. the latest set of x. laevis mirnas were downloaded from mirbase (v21) [] but as only 22 precursors we present in the annotation we conducted whole genome annotation of mirnas. all animal […]

PMCID: 5831913
PMID: 29657296
DOI: 10.3390/ncrna3040025

[…] the mirprof pipeline was used to identify conserved mirna. this approach matches srna libraries with known viridiplantae mature and mirna* deposited in mirbase database release 21 [], using the patman program. novel mirnas were identified by the mircat pipeline using sequences mapped to the available sugarcane sequence [] to find clusters of srna. only new mirna with 21 and 22 nt […]

PMCID: 5650620
PMID: 29085379
DOI: 10.3389/fpls.2017.01712

[…] binding sites from the place () and transfac () databases, as well as other experimentally determined consensus sequences curated from literature, were mapped onto the shp2 upstream region using patman (). the output from patman was converted to a gbrowse annotation track using a script for easy visualization (see materials and methods). we identified a cluster of three carg boxes (potential […]


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PatMaN institution(s)
Max-Planck Institute for Evolutionary Anthropology, Leipzig, Germany

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