Chloroplast Genome Annotation Tools: Prolegomena to the Identification of Inverted Repeats

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 gen...
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Autor*in:	Ante Turudić [verfasserIn] Zlatko Liber [verfasserIn] Martina Grdiša [verfasserIn] Jernej Jakše [verfasserIn] Filip Varga [verfasserIn] Zlatko Šatović [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2022

Schlagwörter:	chloroplast genome annotation inverted repeats repeat identification

Übergeordnetes Werk:	In: International Journal of Molecular Sciences - MDPI AG, 2003, 23(2022), 18, p 10804
Übergeordnetes Werk:	volume:23 ; year:2022 ; number:18, p 10804

Links:	Link aufrufen Link aufrufen Link aufrufen Journal toc Journal toc

DOI / URN:	10.3390/ijms231810804

Katalog-ID:	DOAJ005563763

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allfields	10.3390/ijms231810804 doi (DE-627)DOAJ005563763 (DE-599)DOAJ39f507fa86e641b4b6100bec08fa1208 DE-627 ger DE-627 rakwb eng QH301-705.5 QD1-999 Ante Turudić verfasserin aut Chloroplast Genome Annotation Tools: Prolegomena to the Identification of Inverted Repeats 2022 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier 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. chloroplast genome annotation inverted repeats repeat identification Biology (General) Chemistry Zlatko Liber verfasserin aut Martina Grdiša verfasserin aut Jernej Jakše verfasserin aut Filip Varga verfasserin aut Zlatko Šatović verfasserin aut In International Journal of Molecular Sciences MDPI AG, 2003 23(2022), 18, p 10804 (DE-627)316340715 (DE-600)2019364-6 14220067 nnns volume:23 year:2022 number:18, p 10804 https://doi.org/10.3390/ijms231810804 kostenfrei https://doaj.org/article/39f507fa86e641b4b6100bec08fa1208 kostenfrei https://www.mdpi.com/1422-0067/23/18/10804 kostenfrei https://doaj.org/toc/1661-6596 Journal toc kostenfrei https://doaj.org/toc/1422-0067 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 23 2022 18, p 10804
spelling	10.3390/ijms231810804 doi (DE-627)DOAJ005563763 (DE-599)DOAJ39f507fa86e641b4b6100bec08fa1208 DE-627 ger DE-627 rakwb eng QH301-705.5 QD1-999 Ante Turudić verfasserin aut Chloroplast Genome Annotation Tools: Prolegomena to the Identification of Inverted Repeats 2022 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier 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. chloroplast genome annotation inverted repeats repeat identification Biology (General) Chemistry Zlatko Liber verfasserin aut Martina Grdiša verfasserin aut Jernej Jakše verfasserin aut Filip Varga verfasserin aut Zlatko Šatović verfasserin aut In International Journal of Molecular Sciences MDPI AG, 2003 23(2022), 18, p 10804 (DE-627)316340715 (DE-600)2019364-6 14220067 nnns volume:23 year:2022 number:18, p 10804 https://doi.org/10.3390/ijms231810804 kostenfrei https://doaj.org/article/39f507fa86e641b4b6100bec08fa1208 kostenfrei https://www.mdpi.com/1422-0067/23/18/10804 kostenfrei https://doaj.org/toc/1661-6596 Journal toc kostenfrei https://doaj.org/toc/1422-0067 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 23 2022 18, p 10804
allfields_unstemmed	10.3390/ijms231810804 doi (DE-627)DOAJ005563763 (DE-599)DOAJ39f507fa86e641b4b6100bec08fa1208 DE-627 ger DE-627 rakwb eng QH301-705.5 QD1-999 Ante Turudić verfasserin aut Chloroplast Genome Annotation Tools: Prolegomena to the Identification of Inverted Repeats 2022 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier 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. chloroplast genome annotation inverted repeats repeat identification Biology (General) Chemistry Zlatko Liber verfasserin aut Martina Grdiša verfasserin aut Jernej Jakše verfasserin aut Filip Varga verfasserin aut Zlatko Šatović verfasserin aut In International Journal of Molecular Sciences MDPI AG, 2003 23(2022), 18, p 10804 (DE-627)316340715 (DE-600)2019364-6 14220067 nnns volume:23 year:2022 number:18, p 10804 https://doi.org/10.3390/ijms231810804 kostenfrei https://doaj.org/article/39f507fa86e641b4b6100bec08fa1208 kostenfrei https://www.mdpi.com/1422-0067/23/18/10804 kostenfrei https://doaj.org/toc/1661-6596 Journal toc kostenfrei https://doaj.org/toc/1422-0067 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 23 2022 18, p 10804
allfieldsGer	10.3390/ijms231810804 doi (DE-627)DOAJ005563763 (DE-599)DOAJ39f507fa86e641b4b6100bec08fa1208 DE-627 ger DE-627 rakwb eng QH301-705.5 QD1-999 Ante Turudić verfasserin aut Chloroplast Genome Annotation Tools: Prolegomena to the Identification of Inverted Repeats 2022 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier 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. chloroplast genome annotation inverted repeats repeat identification Biology (General) Chemistry Zlatko Liber verfasserin aut Martina Grdiša verfasserin aut Jernej Jakše verfasserin aut Filip Varga verfasserin aut Zlatko Šatović verfasserin aut In International Journal of Molecular Sciences MDPI AG, 2003 23(2022), 18, p 10804 (DE-627)316340715 (DE-600)2019364-6 14220067 nnns volume:23 year:2022 number:18, p 10804 https://doi.org/10.3390/ijms231810804 kostenfrei https://doaj.org/article/39f507fa86e641b4b6100bec08fa1208 kostenfrei https://www.mdpi.com/1422-0067/23/18/10804 kostenfrei https://doaj.org/toc/1661-6596 Journal toc kostenfrei https://doaj.org/toc/1422-0067 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 23 2022 18, p 10804
allfieldsSound	10.3390/ijms231810804 doi (DE-627)DOAJ005563763 (DE-599)DOAJ39f507fa86e641b4b6100bec08fa1208 DE-627 ger DE-627 rakwb eng QH301-705.5 QD1-999 Ante Turudić verfasserin aut Chloroplast Genome Annotation Tools: Prolegomena to the Identification of Inverted Repeats 2022 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier 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. chloroplast genome annotation inverted repeats repeat identification Biology (General) Chemistry Zlatko Liber verfasserin aut Martina Grdiša verfasserin aut Jernej Jakše verfasserin aut Filip Varga verfasserin aut Zlatko Šatović verfasserin aut In International Journal of Molecular Sciences MDPI AG, 2003 23(2022), 18, p 10804 (DE-627)316340715 (DE-600)2019364-6 14220067 nnns volume:23 year:2022 number:18, p 10804 https://doi.org/10.3390/ijms231810804 kostenfrei https://doaj.org/article/39f507fa86e641b4b6100bec08fa1208 kostenfrei https://www.mdpi.com/1422-0067/23/18/10804 kostenfrei https://doaj.org/toc/1661-6596 Journal toc kostenfrei https://doaj.org/toc/1422-0067 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 23 2022 18, p 10804
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callnumber-first	Q - Science
author	Ante Turudić
spellingShingle	Ante Turudić misc QH301-705.5 misc QD1-999 misc chloroplast genome misc annotation misc inverted repeats misc repeat identification misc Biology (General) misc Chemistry Chloroplast Genome Annotation Tools: Prolegomena to the Identification of Inverted Repeats
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topic_title	QH301-705.5 QD1-999 Chloroplast Genome Annotation Tools: Prolegomena to the Identification of Inverted Repeats chloroplast genome annotation inverted repeats repeat identification
topic	misc QH301-705.5 misc QD1-999 misc chloroplast genome misc annotation misc inverted repeats misc repeat identification misc Biology (General) misc Chemistry
topic_unstemmed	misc QH301-705.5 misc QD1-999 misc chloroplast genome misc annotation misc inverted repeats misc repeat identification misc Biology (General) misc Chemistry
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title_auth	Chloroplast Genome Annotation Tools: Prolegomena to the Identification of Inverted Repeats
abstract	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.
abstractGer	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.
abstract_unstemmed	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.
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title_short	Chloroplast Genome Annotation Tools: Prolegomena to the Identification of Inverted Repeats
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Chloroplast Genome Annotation Tools: Prolegomena to the Identification of Inverted Repeats

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