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Protocols

iMicrobe specifications

Information


Unique identifier OMICS_11139
Name iMicrobe
Restrictions to use None
Data access File download, Browse, Application programming interface
Maintained Yes

iMicrobe citations

 (28)
library_books

Proteorhodopsin variability and distribution in the North Pacific Subtropical Gyre

2018
PMCID: 5864233
PMID: 29476140
DOI: 10.1038/s41396-018-0074-4

[…] entity. Sequence data used in this study are available from the NCBI short read archive under Bioproject no. PRJNA352737, and the metagenomic data products (contigs, genes, peptides) are available at iMicrobe (https://imicrobe.us/project/view/263).In this study, HMMer v 3.0 [] was used to construct profile hidden Markov models (HMM) using known amino-acid sequences for a gene of interest. Three se […]

library_books

Interaction of a dinoflagellate neurotoxin with voltage activated ion channels in a marine diatom

2018
PeerJ
PMCID: 5888156
PMID: 29632739
DOI: 10.7717/peerj.4533

[…] tricornutum (class Bacillariophyceae, (; )). In addition ten diatom transcriptomes (see ) were available either through the Marine Microbial Eukaryote Transcriptome Sequencing Project () deposited at iMicrobe (http://imicrobe.us, accessed June 14, 2015) or National Center for Biotechnology Information (NCBI), of which five belong to the class Bacillariophyceae, one belongs to class Coscinodiscophy […]

library_books

Microbial eukaryotes have adapted to hypoxia by horizontal acquisitions of a gene involved in rhodoquinone biosynthesis

2018
eLife
PMCID: 5953543
PMID: 29697049
DOI: 10.7554/eLife.34292.028

[…] Since only genomic data was available for Proteromonas lacertae, spliceosomal introns were manually predicted based on homology with Blastocystis protein sequences. Sequences were retrieved from the iMicrobe database (Marine Microbial Eukaryotic Transcriptome sSquencing Project)(https://www.imicrobe.us/#/projects/104) and in-house sequencing projects for Mastigamoeba balamuthi, Blastocystis homin […]

library_books

Chloropicophyceae, a new class of picophytoplanktonic prasinophytes

2017
Sci Rep
PMCID: 5656628
PMID: 29070840
DOI: 10.1038/s41598-017-12412-5

[…] ptome Sequencing Program (MMETSP) were selected to determine the phylogenetic placement of Chloropicophyceae based on a multigene alignment. Reads were downloaded from the MMETSP archive (http://data.imicrobe.us/project/view/104) to the ABiMS platform in Roscoff (http://abims.sb-roscoff.fr). The quality of the reads was checked by FastQC v.0.52 (http://www.bioinformatics.babraham.ac.uk/projects/fa […]

library_books

Diatom flagellar genes and their expression during sexual reproduction in Leptocylindrus danicus

2017
BMC Genomics
PMCID: 5654045
PMID: 29061117
DOI: 10.1186/s12864-017-4210-8

[…] hits with an e-value smaller or equal to 1e-10 were considered. Blast results for diatoms only are shown in Additional file : Table S5. Peptide sequences for selected protein hits were retrieved from iMicrobe [] and blasted in public databases (blastp in nr) to confirm protein identity. […]

call_split

Globally Important Haptophyte Algae Use Exogenous Pyrimidine Compounds More Efficiently than Thiamin

2017
MBio
PMCID: 5635689
PMID: 29018119
DOI: 10.1128/mBio.01459-17
call_split See protocol

[…] 18S rRNA gene sequences were retrieved from the MMETSP (https://imicrobe.us/project/view/104) metadata files and aligned using ClustalW. Positions with gaps were masked. Maximum likelihood phylogenetic trees were computed using the general time-reversible model in […]


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iMicrobe funding source(s)
The Gordon Betty Moore Foundation (Grant #4491)

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