IRplus: An Augmented Tool to Detect Inverted Repeats in Plastid Genomes.

Autor:	Díez Menéndez C; Escuela Politécnica Superior, Universidad Autónoma de Madrid, Madrid, Spain., Poczai P; Botany Unit, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland.; Museomics Research Group, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland., Williams B; Department of Computer Science, University of Helsinki, Helsinki, Finland., Myllys L; Botany Unit, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland., Amiryousefi A; Systems Oncology Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland.; Ludwig Center at Harvard and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, Massachusetts, USA.
Jazyk:	angličtina
Zdroj:	Genome biology and evolution [Genome Biol Evol] 2023 Oct 06; Vol. 15 (10).
DOI:	10.1093/gbe/evad177
Abstrakt:	High-throughput sequencing methods have increased the accessibility of plastid genomes, which are crucial for clarifying phylogenetic relationships. Current large sequencing efforts require software tools for routine display of their distinctive quadripartite structure, which is denoted by four junction sites. By concentrating on these junctions and their close vicinity, IRscope has emerged as the standard tool for detection of this structure and creating simplified comparative graphical maps of plastid genomes. Here, we provide an augmented version (IRplus) that encompasses a novel set of functions such as integrated error detection, flexible color schemes, and an upgraded method to detect inverted repeats in genomic sequences. Spanning across the plant tree of life, IRplus allows the quick visualization of various sets of plastid genomes and features, next to smooth interoperability with other widely used annotation file formats and platforms. The IRplus can be accessed at https://irscope.shinyapps.io/IRplus/, and source codes are freely available at https://github.com/AmiryousefiLab/IRplus. (© The Author(s) 2023. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.)
Databáze:	MEDLINE
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