Bioinformatics Tools enables plant genome analysis and hence enables the scientific attraction to the newest inventions.
A Review of Bioinformatics Tools
The ability to detect sequence variability and gene expression was greatly enhanced by next-generation sequencing and microarray. Specific bioinformatics tools are needed to extract information from the raw data.
The NGS pipelines work on three basic levels for human data analysis: sequence generation, reference genome alignment and results in interpretation. During the analysis, NGS data sets unique to the target / whole-genome or RNA-sequencing are widely available for several bio-Informatics methods.
Big data analysis, made possible through high-performance sequencing, was important for system biology, especially in the areas of gene regulatory networks (GRNs).
Scientists have been allowed to develop Next Generation Sequencing (NGS) that has historically been deemed too difficult or too expensive to examine genomes. The study of complex plant genomes, which often have large repeat sequences, remains a challenge.
Therefore, researchers in bioinformatics from the Leibniz Institute of Plant Genetics and Plant Science (IPK), Martin-Luther University Halle-Wittenberg (MLU), and the Leibniz Institute of Plant Biochemistry (IBB) have now released the Kmasker Plants project.
The term “k” is used in bioinformatics to describe a nucleotide of a certain length “k.” Through recognizing and counting sequences of this kind, researchers will measure and assign repetitive sequences in the genome they sample.
As early as 2014, IPK researchers in Gatersleben used this approach to develop the “Kmasker” in silicon tool. Repetitions were detected when the barley genome was characterised (Schmutzer et al., 2014).
The use of NGS is increasingly important, but it is still difficult to compose complex genomes with the results of NGS without problems. That’s why the researchers have just agreed that this first proof of concept project should be resurrected and expanded.
The MLU, the IPK, the Wageningen University & Research and the IPB Halle have been involved in a partnership with Dr. Thomas Schmutzer, formerly of the research team “Bioinformatics and Information Technology” at IPK and now working with the MLU, to redesign and grow “Kmasker plants.”
This collaboration was largely supported by the two service centres “GCBN” and “CiBi” from the German Network for Bioinformatics Infrastructure “de.NBI”.
“Kmasker plants” allows for the rapid and reference-free screening of nucleotide sequences using genome-wide derived k-mers.
In extension to the previous version, the bioinformatics tool now also enables comparative studies between different cultivars or closely related species and supports the identification of sequences suitable as fluorescence in situ hybridization (FISH) probes or CRISPR/Cas9-specific guide RNAs.
Furthermore, “Kmasker plants” has been published with a web service that contains the pre-computed indices for selected economically important crop plants, such as barley or wheat. Dr Schmutzer emphasises that “this tool will enable plant researchers all over the world to test plant genomes and thus, for example, identify repeat free parts of their sequence of interest.”
Instead, he considers that the enhanced functionality allows the identification of sequence candidate regions which, but lack other species in the genome or occur in smaller numbers, have increased in the genome of one species.
It contributes to a phenotypical agronomic difference in various crops. This is a common effect. The Vrn-H2 gene, present in one single copy in winter barley, is an important example and is absent in barley spring lines.
As part of the IPK Crop Analysis Tool Suite (CATS), and thus as part of the De. NBI Service Portal, the web service “Kmasker Plants” is currently available.
Researchers were able to analyze genomes traditionally thought too difficult or too costly with the creation of the next generation series. However, analyzing complex plant genomes, which are also very repeated, remains a task.
There are also now publishing the Kmasker plants (“Kmasker plants”), which enables the detection of repetitive sequences and therefore encourages the study of plants genomes, bioinformatics researcher from the Leibniz Institute of Plant Genetics and Plant Science (IPK), Martin Luthe University of Halle-Wittenberg (MLU) and Leibniz Institute of Plant Biochemtics (IPB).
In bioinformatics, a nucleotide sequence of a certain length ‘k’ is called the word K-mer. When sequences of this type are identified and counted, researchers may measure and attribute replicated sequences in the genome to which they sample.
Researchers at IPK in Gatersleben also used this method as a basis for the production of the silicon tool “Kmasker” in 2014. Repetition was observed when the barley genome was characterized (Schmutzer et al., 2014).
NGS is becoming increasingly relevant, but the error-free composition of complex NGS genomes remains a problem. That is why the researchers recently agreed to resurrect this original demonstration project and extend it. The scientists of the MLU, IPK, Wageningen University & Science, and the IPB Halle worked together closely to redesign and development of “Bioinformatics and Information Technology” under the leadership of Dr. Thomas Schmutzer, who formerly belonged to the research group “Kmasker plants” The two GCBN and CiBi operation centers from the German Bioinformatics Technology Network “de.NBI” have largely sponsored this cooperation.
Bioinformatics Tools enables plant genome analysis