GeoSymbio protocols

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GeoSymbio specifications

Information


Unique identifier OMICS_16527
Name GeoSymbio
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Erik Franklin <>

Publication for GeoSymbio

GeoSymbio in pipeline

2014
PMCID: 4138093
PMID: 25137123
DOI: 10.1371/journal.pone.0103179

[…] at http://technelysium.com.au/) and exported to mega program v.5 where alignments were constructed using muscle . each individual contig was aligned with its2 sequences downloaded from the geosymbio database . its2 types were designated according to similarity to sequences from the geosymbio database and the dgge fingerprint profile. if the dgge profile indicated its2 bands that ran […]


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GeoSymbio in publications

 (14)
PMCID: 5864192
PMID: 29379177
DOI: 10.1038/s41396-018-0046-8

[…] were aligned and trimmed using geneious 6.0 (biomatters ltd). consensus sequences were used for blast searches to identify the closest match in ncbi genbank. sequences were cross-referenced with the geosymbio database []., a second aliquot of the frozen cell suspension was loaded into a hemocytometer to count the total number of dividing symbiodinium cells (doublets) relative to the total number […]

PMCID: 5520142
PMID: 28323278
DOI: 10.1038/ismej.2017.17

[…] were analyzed using dnastar (lasergene, madison, wi, usa) and macvector (accelrys, san diego, ca, usa) and assigned to clades by performing blast searches against the its2 sequence database from geosymbio () or genbank., the data for symbiodinium cell size () was analyzed by one-way analysis of variance between the three size groups after the normality was confirmed by chi-square […]

PMCID: 5315387
PMID: 28212387
DOI: 10.1371/journal.pone.0172285

[…] level using a blast search via the website of the dna data bank of japan (ddbj; http://www.ddbj.nig.ac.jp/index-j.html). then, each clade clone was further classified into its2 types according to geosymbio []., positive qpcr results were obtained for 186 tridacnine clam individuals, 93 t. crocea and 93 t. squamosa specimens (qpcr failed for three individuals of each species), and clear […]

PMCID: 5732543
PMID: 29255647
DOI: 10.7717/peerj.4055

[…] sequence data were edited and assembled using atsq, version 6.0.1 (genetyx co., tokyo, japan), and identified through blast searches of the international nucleotide sequence database (insd) and the geosymbio database (), which provides alignments of symbiodinium nrits2 sequences that were published between 1982 and 2012., growth of the corals was estimated from the mean values of their skeleton […]

PMCID: 4753424
PMID: 26876092
DOI: 10.1038/srep20717

[…] of the 20 distinct operational taxonomic units (otu) identified, ten were assigned to subclade d1 and two to subclade c3 (both found in one colony of p. sinensis) based on the top blast+ hits to the geosymbio database. it was not possible to assign the remaining seven otus to subclade level but they all belonged to clade d., between may and august 2010 singapore’s reefs underwent a major […]


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GeoSymbio institution(s)
Hawaii Institute of Marine Biology, School of Ocean and Earth Science and Technology, University of Hawaii at Manoa, Kaneohe, HI, USA
GeoSymbio funding source(s)
This work was supported by the National Marine Sanctuary Program (memorandum of agreement 2005-008⁄66882), the US Environmental Protection Agency Science To Achieve Results (STAR) PhD Fellowship (FP917096 and FP917199), the US National Science Foundation (NSF) for grants through Biological Oceanography (OCE- 0752604, OCE-1041673) and the Long-Term Ecological Research (LTER) program (NSF 04-17412).

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