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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 citations

 (66)
library_books

Towards annotating the plant epigenome: the Arabidopsis thaliana small RNA locus map

2018
Sci Rep
PMCID: 5910406
PMID: 29679055
DOI: 10.1038/s41598-018-24515-8

[…] iring perfect matching; sequences not overlapping with the adaptor on the 3′ end were discarded. The remaining reads were then size selected, keeping only 15–30 nt long reads. These were mapped using PatMaN against the Arabidopsis thaliana genome (TAIR10), allowing no mismatches and reporting all multimatch locations.Reads were also aligned to the miRNA hairpin structures in Arabidopsis thaliana r […]

call_split

Small RNA populations revealed by blocking rRNA fragments in Drosophila melanogaster reproductive tissues

2018
PLoS One
PMCID: 5825024
PMID: 29474379
DOI: 10.1371/journal.pone.0191966
call_split See protocol

[…] size 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 […]

library_books

Contemporary Strategies in the Management of Civilian Abdominal Vascular Trauma

2018
PMCID: 5826055
PMID: 29516005
DOI: 10.3389/fsurg.2018.00007

[…] vel, 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 from […]

library_books

microRNAs associated with early neural crest development in Xenopus laevis

2018
BMC Genomics
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 mi […]

library_books

Roles of Non Coding RNA in Sugarcane Microbe Interaction

2017
Noncoding RNA
PMCID: 5831913
PMID: 29657296
DOI: 10.3390/ncrna3040025

[…] RNAs. 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 and that sh […]

library_books

Redundant CArG Box Cis motif Activity Mediates SHATTERPROOF2 Transcriptional Regulation during Arabidopsis thaliana Gynoecium Development

2017
Front Plant Sci
PMCID: 5650620
PMID: 29085379
DOI: 10.3389/fpls.2017.01712

[…] Binding sites from PLACE (), AGRIS () and TRANSFAC () databases were mapped to the SHP2 genomic locus including 3kb upstream of the SHP2 translation start site using PatMaN software (). Output results files from PatMaN were converted to annotation tracks for viewing Genome Browser in TAIR using python scripts. All scripts are accessible through github: https://git […]

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

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