ChloroMitoSSRDB 2.00: More genomes, more repeats, unifying SSRs search patterns and on-the-fly repeat detection

Sablok, G; Padma Raju, GV; Mudunuri, SB; Prabha, R; Singh, DP; Baev, V; Yahubyan, G; Ralph, PJ; La Porta, N

ChloroMitoSSRDB 2.00: More genomes, more repeats, unifying SSRs search patterns and on-the-fly repeat detection

Sablok, G

Padma Raju, GV Mudunuri, SB Prabha, R Singh, DP Baev, V Yahubyan, G Ralph, PJ

La Porta, N

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Publication Type:: Journal Article
Citation:: Database, 2015, 2015
Issue Date:: 2015-01-01

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Field	Value	Language
dc.contributor.author	Sablok, G https://orcid.org/0000-0002-4157-9405	en_US
dc.contributor.author	Padma Raju, GV	en_US
dc.contributor.author	Mudunuri, SB	en_US
dc.contributor.author	Prabha, R	en_US
dc.contributor.author	Singh, DP	en_US
dc.contributor.author	Baev, V	en_US
dc.contributor.author	Yahubyan, G	en_US
dc.contributor.author	Ralph, PJ https://orcid.org/0000-0002-3103-7346	en_US
dc.contributor.author	La Porta, N	en_US
dc.date.available	2015-08-17	en_US
dc.date.issued	2015-01-01	en_US
dc.identifier.citation	Database, 2015, 2015	en_US
dc.identifier.issn	1758-0463	en_US
dc.identifier.uri	http://hdl.handle.net/10453/37631
dc.description.abstract	© The Author(s) 2015. Published by Oxford University Press. Organelle genomes evolve rapidly as compared with nuclear genomes and have been widely used for developing microsatellites or simple sequence repeats (SSRs) markers for delineating phylogenomics. In our previous reports, we have established the largest repository of organelle SSRs, ChloroMitoSSRDB, which provides access to 2161 organelle genomes (1982 mitochondrial and 179 chloroplast genomes) with a total of 5838 perfect chloroplast SSRs, 37 297 imperfect chloroplast SSRs, 5898 perfect mitochondrial SSRs and 50 355 imperfect mitochondrial SSRs across organelle genomes. In the present research, we have updated ChloroMitoSSRDB by systematically analyzing and adding additional 191 chloroplast and 2102 mitochondrial genomes. With the recent update, ChloroMitoSSRDB 2.00 provides access to a total of 4454 organelle genomes displaying a total of 40 653 IMEx Perfect SSRs (11 802 Chloroplast Perfect SSRs and 28 851 Mitochondria Perfect SSRs), 275 981 IMEx Imperfect SSRs (78 972 Chloroplast Imperfect SSRs and 197 009 Mitochondria Imperfect SSRs), 35 250 MISA (MIcroSAtellite identification tool) Perfect SSRs and 3211 MISA Compound SSRs and associated information such as location of the repeats (coding and non-coding), size of repeat, motif and length polymorphism, and primer pairs. Additionally, we have integrated and made available several in silico SSRs mining tools through a unified web-portal for in silico repeat mining for assembled organelle genomes and from next generation sequencing reads. ChloroMitoSSRDB 2.00 allows the end user to perform multiple SSRs searches and easy browsing through the SSRs using two repeat algorithms and provide primer pair information for identified SSRs for evolutionary genomics.	en_US
dc.relation.ispartof	Database	en_US
dc.relation.isbasedon	10.1093/database/bav084	en_US
dc.subject.mesh	Plants	en_US
dc.subject.mesh	Sequence Analysis, DNA	en_US
dc.subject.mesh	Microsatellite Repeats	en_US
dc.subject.mesh	Internet	en_US
dc.subject.mesh	Databases, Genetic	en_US
dc.subject.mesh	Genome, Chloroplast	en_US
dc.subject.mesh	Genome, Mitochondrial	en_US
dc.subject.mesh	Molecular Sequence Annotation	en_US
dc.title	ChloroMitoSSRDB 2.00: More genomes, more repeats, unifying SSRs search patterns and on-the-fly repeat detection	en_US
dc.type	Journal Article
utslib.citation.volume	2015	en_US
utslib.for	0804 Data Format	en_US
utslib.for	0807 Library and Information Studies	en_US
pubs.embargo.period	Not known	en_US
pubs.organisational-group	/University of Technology Sydney
pubs.organisational-group	/University of Technology Sydney/Faculty of Science
pubs.organisational-group	/University of Technology Sydney/Strength - C3 - Climate Change Cluster
utslib.copyright.status	open_access
pubs.publication-status	Published	en_US
pubs.volume	2015	en_US

Abstract:

© The Author(s) 2015. Published by Oxford University Press. Organelle genomes evolve rapidly as compared with nuclear genomes and have been widely used for developing microsatellites or simple sequence repeats (SSRs) markers for delineating phylogenomics. In our previous reports, we have established the largest repository of organelle SSRs, ChloroMitoSSRDB, which provides access to 2161 organelle genomes (1982 mitochondrial and 179 chloroplast genomes) with a total of 5838 perfect chloroplast SSRs, 37 297 imperfect chloroplast SSRs, 5898 perfect mitochondrial SSRs and 50 355 imperfect mitochondrial SSRs across organelle genomes. In the present research, we have updated ChloroMitoSSRDB by systematically analyzing and adding additional 191 chloroplast and 2102 mitochondrial genomes. With the recent update, ChloroMitoSSRDB 2.00 provides access to a total of 4454 organelle genomes displaying a total of 40 653 IMEx Perfect SSRs (11 802 Chloroplast Perfect SSRs and 28 851 Mitochondria Perfect SSRs), 275 981 IMEx Imperfect SSRs (78 972 Chloroplast Imperfect SSRs and 197 009 Mitochondria Imperfect SSRs), 35 250 MISA (MIcroSAtellite identification tool) Perfect SSRs and 3211 MISA Compound SSRs and associated information such as location of the repeats (coding and non-coding), size of repeat, motif and length polymorphism, and primer pairs. Additionally, we have integrated and made available several in silico SSRs mining tools through a unified web-portal for in silico repeat mining for assembled organelle genomes and from next generation sequencing reads. ChloroMitoSSRDB 2.00 allows the end user to perform multiple SSRs searches and easy browsing through the SSRs using two repeat algorithms and provide primer pair information for identified SSRs for evolutionary genomics.

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http://hdl.handle.net/10453/37631