scholarly journals LtrDetector: A modern tool-suite for detecting long terminal repeat retrotransposons de-novo on the genomic scale

2018 ◽  
Author(s):  
Joseph D Valencia ◽  
Hani Z Girgis
Keyword(s):  
Long Terminal Repeat ◽  
Large Scale ◽  
De Novo ◽  
False Positive Rate ◽  
Long Terminal Repeat Retrotransposons ◽  
Terminal Repeat ◽  
Plant Genomes ◽  
Positive Rate ◽  
Genomic Scale ◽  
Species Specific

AbstractLong terminal repeat retrotransposons are the most abundant transposons in plants. They play important roles in alternative splicing, recombination, gene regulation, and genomic evolution. Large-scale sequencing projects for plant genomes are currently underway. Software tools are important for annotating long terminal repeat retrotransposons in these newly available genomes. However, the available tools are not very sensitive to known elements and perform inconsistently on different genomes. Some are hard to install or obsolete. They may struggle to process large plant genomes. None are concurrent or have features to support manual review of new elements. To overcome these limitations, we developed LtrDetector, which uses signal-processing techniques. LtrDetector is easy to install and use. It is not species specific. It utilizes multi-core processors available in personal computers. It is more sensitive than other tools by 14.4%–50.8% while maintaining a low false positive rate on six plant genomes.

scholarly journals LTR_FINDER_parallel: parallelization of LTR_FINDER enabling rapid identification of long terminal repeat retrotransposons

Mobile DNA ◽  
2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Shujun Ou ◽  
Ning Jiang
Keyword(s):  
Triticum Aestivum ◽  
Long Terminal Repeat ◽  
Bread Wheat ◽  
Repetitive Sequences ◽  
Long Terminal Repeat Retrotransposons ◽  
Rapid Identification ◽  
Terminal Repeat ◽  
Parallel Operation ◽  
Ltr Retrotransposons ◽  
Plant Genomes

AbstractAnnotation of plant genomes is still a challenging task due to the abundance of repetitive sequences, especially long terminal repeat (LTR) retrotransposons. LTR_FINDER is a widely used program for the identification of LTR retrotransposons but its application on large genomes is hindered by its single-threaded processes. Here we report an accessory program that allows parallel operation of LTR_FINDER, resulting in up to 8500X faster identification of LTR elements. It takes only 72 min to process the 14.5 Gb bread wheat (Triticum aestivum) genome in comparison to 1.16 years required by the original sequential version. LTR_FINDER_parallel is freely available at https://github.com/oushujun/LTR_FINDER_parallel.

scholarly journals LTR_FINDER_parallel: parallelization of LTR_FINDER enabling rapid identification of long terminal repeat retrotransposons

2019 ◽  
Author(s):  
Shujun Ou ◽  
Ning Jiang
Keyword(s):  
Triticum Aestivum ◽  
Long Terminal Repeat ◽  
Bread Wheat ◽  
Repetitive Sequences ◽  
Long Terminal Repeat Retrotransposons ◽  
Rapid Identification ◽  
Terminal Repeat ◽  
Parallel Operation ◽  
Ltr Retrotransposons ◽  
Plant Genomes

AbstractSummaryAnnotation of plant genomes is still a challenging task due to the abundance of repetitive sequences, especially long terminal repeat (LTR) retrotransposons. LTR_FINDER is a widely used program for identification of LTR retrotransposons but its application on large genomes is hindered by its single threaded processes. Here we report an accessory program that allows parallel operation of LTR_FINDER, resulting up to 8,500X faster identification of LTR elements. It takes only 72 minutes to process the 14.5 Gb bread wheat (Triticum aestivum) genome in comparison to 1.16 years required by the original sequential version.AvailabilityLTR_FINDER_parallel is freely available at https://github.com/oushujun/[email protected]

Identification of and Correction for Publication Bias: Comment

2019 ◽  
Author(s):  
Amanda Kvarven ◽  
Eirik Strømland ◽  
Magnus Johannesson
Keyword(s):  
Publication Bias ◽  
False Positive ◽  
Large Scale ◽  
Meta Analysis ◽  
False Positive Rate ◽  
Effect Sizes ◽  
Replication Studies ◽  
Moderate Reduction ◽  
Positive Rate ◽  
Meta Analyses

Andrews & Kasy (2019) propose an approach for adjusting effect sizes in meta-analysis for publication bias. We use the Andrews-Kasy estimator to adjust the result of 15 meta-analyses and compare the adjusted results to 15 large-scale multiple labs replication studies estimating the same effects. The pre-registered replications provide precisely estimated effect sizes, which do not suffer from publication bias. The Andrews-Kasy approach leads to a moderate reduction of the inflated effect sizes in the meta-analyses. However, the approach still overestimates effect sizes by a factor of about two or more and has an estimated false positive rate of between 57% and 100%.

scholarly journals Efficient Detection of Large-Scale Multimedia Network Information Data Anomalies Based on the Rule-Extracting Matrix Algorithm

2021 ◽  
Vol 2021 ◽  
pp. 1-7
Author(s):  
Jie Zhao
Keyword(s):  
Large Scale ◽  
False Positive Rate ◽  
Detection Accuracy ◽  
Network Information ◽  
Matrix Algorithm ◽  
Efficient Detection ◽  
Sample Data ◽  
Multimedia Social Networks ◽  
Positive Rate ◽  
Rule Extracting

With the continuous development of multimedia social networks, online public opinion information is becoming more and more popular. The rule extraction matrix algorithm can effectively improve the probability of information data to be tested. The network information data abnormality detection is realized through the probability calculation, and the prior probability is calculated, to realize the detection of abnormally high network data. Practical results show that the rule-extracting matrix algorithm can effectively control the false positive rate of sample data, the detection accuracy is improved, and it has efficient detection performance.

scholarly journals Bloom Filter-Based Secure Data Forwarding in Large-Scale Cyber-Physical Systems

2015 ◽  
Vol 2015 ◽  
pp. 1-12
Author(s):  
Siyu Lin ◽  
Hao Wu
Keyword(s):  
False Positive ◽  
Large Scale ◽  
False Positive Rate ◽  
Bloom Filter ◽  
Cyber Physical Systems ◽  
Security Requirements ◽  
Data Forwarding ◽  
Physical Systems ◽  
Secure Data ◽  
Positive Rate

Cyber-physical systems (CPSs) connect with the physical world via communication networks, which significantly increases security risks of CPSs. To secure the sensitive data, secure forwarding is an essential component of CPSs. However, CPSs require high dimensional multiattribute and multilevel security requirements due to the significantly increased system scale and diversity, and hence impose high demand on the secure forwarding information query and storage. To tackle these challenges, we propose a practical secure data forwarding scheme for CPSs. Considering the limited storage capability and computational power of entities, we adopt bloom filter to store the secure forwarding information for each entity, which can achieve well balance between the storage consumption and query delay. Furthermore, a novel link-based bloom filter construction method is designed to reduce false positive rate during bloom filter construction. Finally, the effects of false positive rate on the performance of bloom filter-based secure forwarding with different routing policies are discussed.

scholarly journals The site-specific ribosomal DNA insertion element R1Bm belongs to a class of non-long-terminal-repeat retrotransposons.

1988 ◽  
Vol 8 (1) ◽  
pp. 114-123 ◽  
Author(s):  
Y Xiong ◽  
T H Eickbush
Keyword(s):  
Amino Acids ◽  
Reverse Transcriptase ◽  
Long Terminal Repeat ◽  
Ribosomal Dna ◽  
Long Terminal Repeat Retrotransposons ◽  
Amino Acid Sequences ◽  
Terminal Repeat ◽  
Type I ◽  
Sequence Specificity ◽  
Insertion Element

Two types of insertion elements, R1 and R2 (previously called type I and type II), are known to interrupt the 28S ribosomal genes of several insect species. In the silkmoth, Bombyx mori, each element occupies approximately 10% of the estimated 240 ribosomal DNA units, while at most only a few copies are located outside the ribosomal DNA units. We present here the complete nucleotide sequence of an R1 insertion from B. mori (R1Bm). This 5.1-kilobase element contains two overlapping open reading frames (ORFs) which together occupy 88% of its length. ORF1 is 461 amino acids in length and exhibits characteristics of retroviral gag genes. ORF2 is 1,051 amino acids in length and contains homology to reverse transcriptase-like enzymes. The analysis of 3' and 5' ends of independent isolates from the ribosomal locus supports the suggestion that R1 is still functioning as a transposable element. The precise location of the element within the genome implies that its transposition must occur with remarkable insertion sequence specificity. Comparison of the deduced amino acid sequences from six retrotransposons, R1 and R2 of B. mori, I factor and F element of Drosophila melanogaster, L1 of Mus domesticus, and Ingi of Trypanosoma brucei, reveals a relatively high level of sequence homology in the reverse transcriptase region. Like R1, these elements lack long terminal repeats. We have therefore named this class of related elements the non-long-terminal-repeat (non-LTR) retrotransposons.

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