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proTRAC specifications

Information


Unique identifier OMICS_04874
Name proTRAC
Alternative name probabilistic TRacking and Analysis of Clusters
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for probabilistic TRacking and Analysis of Clusters

proTRAC citations

 (13)
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

[…] nd 137 hairpins which clustered into 70 groups (102 unique mature miRNAs) were selected which met our criterion, these were designated as novel X. laevis miRNAs. piRNA clustering and analysis we used probabilistic tracking and analysis of clusters (ProTRAC) []. […]

call_split

Assessment of piRNA biogenesis and function in testicular germ cell tumors and their precursor germ cell neoplasia in situ

2018
BMC Cancer
PMCID: 5755174
PMID: 29301509
DOI: 10.1186/s12885-017-3945-6
call_split See protocol

[…] ismatches allowed and were used to calculate TE-specific ping-pong Z-score and distribution of reads along the consensi.Probabilistic piRNA cluster calling was done with TBr2_duster.pl/sRNAmapper.pl/ proTRAC_2.1.2.pl pipeline by Rosenkranz and Zischler [, ] with proTRAC parameters as follows: -pdens 0.05 -1Tor10A 0.1 -1Tand10A 0.1 -clstrand 0.5 -clsplit 0.05. Finally, a list of 1299 of human piRNA […]

library_books

Effective computational detection of piRNAs using n gram models and support vector machine

2017
BMC Bioinformatics
PMCID: 5751586
PMID: 29297285
DOI: 10.1186/s12859-017-1896-1

[…] e most piRNAs are derived from genomic piRNA clusters [–], the second class utilizes the information on clustering locus for piRNA detection. Among the approaches based on clustering locus of piRNAs, proTRAC [] can identify piRNA clusters and piRNAs from a small RNA-seq dataset through a probabilistic analysis of mapped sequence reads. Furthermore, piClust [] uses a density-based clustering method […]

library_books

Characterization of the piRNA pathway during development of the sea anemone Nematostella vectensis

2017
RNA Biol
PMCID: 5731801
PMID: 28783426
DOI: 10.1080/15476286.2017.1349048

[…] piRNA cluster detection was performed on Nematostella piRNAs using the proTRAC pipeline version 2.1 with the options protrac_nv (Supplemental Table S3) for each developmental stage. Clusters were then merged using the bedtools suite, resulting in 457 clusters. Unassigned […]

call_split

Small RNA sequencing of cryopreserved semen from single bull revealed altered miRNAs and piRNAs expression between High and Low motile sperm populations

2017
BMC Genomics
PMCID: 5209821
PMID: 28052756
DOI: 10.1186/s12864-016-3394-7
call_split See protocol

[…] ware.html) was used to assign read counts of multiple mapping sequences according to estimated local transcription rates based on uniquely mapping sequences.piRNA cluster detection was performed with proTRAC version 2.1 [, ], imposing a piRNA length of 26 to 33 bp and a minimum cluster length of 5000 bp. Genes falling within the detected clusters were retrieved according to Bt3.1 NCBI annotation, […]

library_books

Germ cell and tumor associated piRNAs in the medaka and Xiphophorus melanoma models

2016
BMC Genomics
PMCID: 4869193
PMID: 27183847
DOI: 10.1186/s12864-016-2697-z

[…] found different expression patterns in germline cells, different melanoma types and healthy skin.Prior to developing our own piRNA clustering pipeline we tested two already publicly available tools, proTRAC [] and piClust []. We excluded piClust, because of the restriction to selected genomes, file size and the limited number of multiple mapping sites per read. Using our dataset proTRAC resulted […]

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proTRAC institution(s)
Institute of Anthropology, Johannes Gutenberg-University Mainz, Mainz, Germany

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