Biology subjects

Ecovoiu, A. A.

Publications and source records attributed to Ecovoiu, A. A..

4 recordsLinked to original sources

bioRxiv2023

qDATA - an R application implementing a practical framework for analyzing quantitative Real-Time PCR data

Gene expression assays that are based on quantitative real-time PCR (qRT-PCR) method are still very popular, therefore, we developed qDATA, a modern open-source R based bioinformatics application that offers a quick and intuitive analysis of raw cycle threshold (Ct) values. The application relies on a straightforward specific data input consisting in Ct values and a few other mandatory fields specifying the experimental and control groups, as well as the target and house-keeping genes. Afterwards, it automatically performs descriptive statistics, normality and statistical testing on 2-{Delta}Ct (or {Delta}Ct) and 2-{Delta}{Delta}Ct terms calculated with Livaks method. Each computation is indicated in dedicated tabs that display their output consisting in dynamic data tables and publishing quality graphs. We also detail a qRT-PCR data analysis framework that depends on performing exhaustive {Delta}Ct calculations within discrete biological replicates (BRs). The Livak formula is used for the complete sets of available data. These prerequisites arguably lead to an improved data analysis and statistical relevance. In order to maximize the relevance of the results we recommend using at least three BRs and three technical replicates. The efficiency of our computing approach was tested with qDATA using input Ct values corresponding to immune related gene expression evaluated in experimental infection of Drosophila melanogaster and summer versus winter Apis mellifera workers, respectively. Our results reveal that our working strategy is very reliable and highlight the efficacy and performance of qDATA application.

genetics↗

bioRxiv2022

A bioinformatics pipeline for the assessment of the evolutionary relationship of some Drosophila species based on class II transposons mapping

Transposons are mobile DNA sequences, known for their ability to insert into other locations in the genome. Genome sequencing allowed the identification of the high content of transposons in various model organisms. Here, we present a bioinformatics pipeline developed to estimate the evolutionary relationship between Drosophila melanogaster and other Drosophilidae based on the comparative analysis of the presence and distribution of class II transposons. Our study reveals that the presence and distribution of transposons hobo, HB, Tc1, Tc1-2, hopper and Bari1 points to close evolutionary relationship among D. melanogaster, D. simulans, D. sechellia and D. yakuba, which is in accordance with other data available in literature.

bioinformatics↗

bioRxiv2020

Genome ARTIST_v2 software - a support for annotation of class II natural transposons in new sequenced genomes

Transposon annotation is a very dynamic field of genomics and various tools assigned to support this bioinformatics endeavor were reported. Genome ARTIST (GA) software was initially developed for mapping artificial transposons mobilized during insertional mutagenesis projects. Now, the new functions of GA_v2 qualify it as an effective companion for mapping and annotation of class II natural transposons in assembled genomes, contigs or sequencing reads. Tabular export of mapping and annotation data for subsequent high-throughput data analysis, the export of a list of flanking sequences around either the coordinates of insertion or around the target site duplications (TSDs) and generation of a consensus sequence for the respective flanking sequences are all key assets of GA_v2. Additionally, we developed two accompanying short scripts that enable the user to annotate transposons existent in assembled genomes and to use various annotation offered by FlyBase for Drosophila melanogaster genome. Herein, we present the applicability of GA_v2 for a preliminary annotation of the class II transposon P-element in the genome of D. melanogaster strain Horezu, Romania, which was sequenced with Nanopore technology in our laboratory. Our results point that GA_v2 is a reliable tool to be integrated in pipelines designed to perform transposon annotation in new sequenced genomes. GA_v2 is open source software compatible with Ubuntu, Mac OS and Windows and is available at https://github.com/genomeartist/genomeartist and at www.genomeartist.ro.

bioinformatics↗

bioRxiv2019

Insertions of P{lacW} and P{EP} artificial transposons on the chromosomal divisions of Drosophila melanogaster are not randomly distributed

Herein we describe the distribution of P{lacW} and P{EP} artificial transposons in the genome of Drosophila melanogaster. A total number of 5,560 P{lacW} and 3,786 P{EP} insertions available on FlyBase were extracted from this database and ordered according to the chromosomal regions they hit. Comparative bioinformatics analysis revealed that the insertions patterns are similar for P{lacW} and P{EP}. The two patterns are significantly correlated for chromosomes X, 2L, 2R and 3L, but not for 3R.\n\nFourier analysis revealed a periodic behaviour in the distribution of insertions, which approximates insertional hotspots. Our results raise questions concerning if and how the local chromosomal landscape affects the insertion patterns of different but related transposons.

genomics↗