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Algal Functional Annotation Tool specifications

Information


Unique identifier OMICS_02226
Name Algal Functional Annotation Tool
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for Algal Functional Annotation Tool

Algal Functional Annotation Tool citations

 (8)
library_books

Population size changes and selection drive patterns of parallel evolution in a host–virus system

2018
Nat Commun
PMCID: 5923231
PMID: 29703896
DOI: 10.1038/s41467-018-03990-7

[…] variants–was performed by searching for each gene (by protein id = gene id) the corresponding kog id, function and kog name by using the jgi genome portal. go enrichment was performed using the algal functional annotation tool., all statistics were performed using r version 3.3.2 and the lme4 package., the phenotypic and population density data that support the findings of this study […]

library_books

Cellular toxicity pathways of inorganic and methyl mercury in the green microalga Chlamydomonas reinhardtii

2017
Sci Rep
PMCID: 5556115
PMID: 28808314
DOI: 10.1038/s41598-017-08515-8

[…] mapman (version 3.6.0rc1), . wilcoxon test were used to identify most strongly dysregulated categories in each treatment (p < 0.05). gene information was also retrieved using algeapath and the algal functional annotation tool, ., to validate the rnaseq, rt-qpcr analysis was performed. details can be found in the supporting information., the effects of ihg and mehg on algal physiology […]

library_books

miRNAs in the alga Chlamydomonas reinhardtii are not phylogenetically conserved and play a limited role in responses to nutrient deprivation

2017
Sci Rep
PMCID: 5511227
PMID: 28710366
DOI: 10.1038/s41598-017-05561-0

[…] functions of the predicted targets were evaluated by using the annotations of chlamydomonas genes (if available) as well as conserved protein domains. functional annotations were obtained with the algal functional annotation tool and are mostly based on those in phytozome v11., transcriptome sequencing was performed on rna samples isolated from maa7-ir44s and mut-20 grown photoautotrophically […]

call_split

Stress responses of the oil producing green microalga Botryococcus braunii Race B

2016
PeerJ
PMCID: 5144741
PMID: 27957393
DOI: 10.7717/peerj.2748
call_split See protocol

[…] b. braunii. additionally, c. reinhardtii genes classified by their functional annotations as defense, stress, or cell death related were used to identify orthologous sequences in b. braunii with the algal functional annotation tool () in the b. braunii race b transcriptome database housed at the university of california, los angeles (http://pathways-pellegrini.mcdb.ucla.edu/botryo1/). […]

library_books

Molecular toxicity of cerium oxide nanoparticles to the freshwater alga Chlamydomonas reinhardtii is associated with supra environmental exposure concentrations

2015
PMCID: 4819577
PMID: 25740379
DOI: 10.3109/17435390.2014.1002868

[…] signal data were analysed using genespring vgx7.3 (agilent technologies), multiexperimental viewer (mev) v4.7 and ge workbench, while sam analysis was carried out within mev. annotation enrichment (algal functional annotation tool and blast2go) compared transcripts statistically significantly altered in expression, as determined by sam, with the list of all detected transcripts., supporting […]

library_books

System level network analysis of nitrogen starvation and recovery in Chlamydomonas reinhardtii reveals potential new targets for increased lipid accumulation

2014
Biotechnol Biofuels
PMCID: 4320484
PMID: 25663847
DOI: 10.1186/s13068-014-0171-1

[…] for this work. protein functions were identified using the biomart tool available at phytozome (http://www.phytozome.org), mercator (http://mapman.gabipd.org/web/guest/app/mercator), and the algal functional annotation tool []., the identified proteins were quantitated by a label-free approach based on total ion count followed by an nsaf normalization […]


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Algal Functional Annotation Tool institution(s)
Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA, USA

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