Algal Functional Annotation Tool protocols

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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 in pipeline

2016
PMCID: 5144741
PMID: 27957393
DOI: 10.7717/peerj.2748

[…] 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/). […]


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Algal Functional Annotation Tool in publications

 (7)
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 […]

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 […]

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 […]

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 […]

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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