Chloroplast genome annotation tools : prolegomena to the identification of inverted repeats

Turudić, Ante (avtor), Liber, Zlatko (avtor), Grdiša, Martina (avtor), Jakše, Jernej (avtor), Varga, Filip (avtor), Šatović, Zlatko (avtor)

The development of next-generation sequencing technology and the increasing amount of sequencing data have brought the bioinformatic tools used in genome assembly into focus. The final step of the process is genome annotation, which works on assembled genome sequences to identify the location of genome features. In the case of organelle genomes, specialized annotation tools are used to identify organelle genes and structural features. Numerous annotation tools target chloroplast sequences. Most chloroplast DNA genomes have a quadripartite structure caused by two copies of a large inverted repeat. We investigated the strategies of six annotation tools (Chloë, Chloroplot, GeSeq, ORG.Annotate, PGA, Plann) for identifying inverted repeats and analyzed their success using publicly available complete chloroplast sequences of taxa belonging to the asterid and rosid clades. The annotation tools use two different approaches to identify inverted repeats, using existing general search tools or implementing stand-alone solutions. The chloroplast sequences studied show that there are different types of imperfections in the assembled data and that each tool performs better on some sequences than the others.

• Jezik: Angleški jezik
• Ključne besede: chloroplast genome, annotation, inverted repeats, repeat identification
• Vrsta gradiva: Članek v reviji
• Tipologija: 1.01 - Izvirni znanstveni članek
• Organizacija: BF - Biotehniška fakulteta
• Status publikacije: Objavljeno
• Različica publikacije: Objavljena publikacija
• Leto izida: 2022
• Št. strani: 19 str.
• Številčenje: Vol. 23, no. 18, art. 10804
• PID: 20.500.12556/RUL-141760
• UDK: 577.2
• ISSN pri članku: 1422-0067
• DOI: 10.3390/ijms231810804
• COBISS.SI-ID: 124702211
• Datum objave v RUL: 07.10.2022

TURUDIĆ, Ante, LIBER, Zlatko, GRDIŠA, Martina, JAKŠE, Jernej, VARGA, Filip in ŠATOVIĆ, Zlatko, 2022, Chloroplast genome annotation tools : prolegomena to the identification of inverted repeats. International journal of molecular sciences [na spletu]. 2022. Vol. 23, no. 18,  10804. [Dostopano 21 april 2025]. DOI 10.3390/ijms231810804. Pridobljeno s: https://repozitorij.uni-lj.si/IzpisGradiva.php?lang=slv&id=141760

Gradivo je del revije

• Naslov: International journal of molecular sciences
• Skrajšan naslov: Int. j. mol. sci.
• Založnik: MDPI
• ISSN: 1422-0067
• COBISS.SI-ID: 2779162

Licence

• Licenca: CC BY 4.0, Creative Commons Priznanje avtorstva 4.0 Mednarodna
• Povezava: http://creativecommons.org/licenses/by/4.0/deed.sl
• Opis: To je standardna licenca Creative Commons, ki daje uporabnikom največ možnosti za nadaljnjo uporabo dela, pri čemer morajo navesti avtorja.

Sekundarni jezik

• Jezik: Slovenski jezik
• Ključne besede: kloroplast, genom kloroplasta, bioinformatika, sekvenciranje genoma, molekularne tehnike