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MMETSP specifications

Information


Unique identifier OMICS_14304
Name MMETSP
Alternative name Marine Microbial Eukaryotic Transcriptome Sequencing Project
Restrictions to use None
Community driven No
Data access Browse
User data submission Not allowed
Maintained No

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Publication for Marine Microbial Eukaryotic Transcriptome Sequencing Project

MMETSP citations

 (56)
call_split

Endocytosis mediated siderophore uptake as a strategy for Fe acquisition in diatoms

2018
Sci Adv
PMCID: 5955625
PMID: 29774236
DOI: 10.1126/sciadv.aar4536
call_split See protocol

[…] The ISIP1 protein sequence (Phatr3_J55031) was used as the seed sequence for BLASTp analysis against a curated library comprising all protein sequences in UniRef, the MMETSP (), and all additional sequences hosted on the JGI portal. This composite database, described by Dorrell et al. (), is more extensive than any individual resource. Sequences retrieved with a th […]

library_books

Gene refashioning through innovative shifting of reading frames in mosses

2018
Nat Commun
PMCID: 5908804
PMID: 29674719
DOI: 10.1038/s41467-018-04025-x

[…] charophytes Nitella hyalina and Closterium peracerosum–strigosum–littorale complex in NCBI, as well as the over 650 transcriptomes in the Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP) (http://marinemicroeukaryotes.org/resources). BLAST search of 1KP database using Marchantia and Sphagnum Hr protein sequences (JGI IDs: Mapoly0112s0056.1 and Sphfalx0048s0034.1) as query ident […]

library_books

Recurrent acquisition of cytosine methyltransferases into eukaryotic retrotransposons

2018
Nat Commun
PMCID: 5890265
PMID: 29632298
DOI: 10.1038/s41467-018-03724-9

[…] the complete domain architecture using Hmmscan with PfamA database as obtained in March 2015. For the dinoflagellate species without reference genome, we downloaded transcriptome assemblies from the MMETSP project and we used Transdecoder to obtain coding sequences. Reference retrotransposons sequences were obtained from RepBase (download February 2014). Viral sequences were obtained from NCBI no […]

call_split

Multispecies reconstructions uncover widespread conservation, and lineage specific elaborations in eukaryotic mRNA metabolism

2018
PLoS One
PMCID: 5862402
PMID: 29561870
DOI: 10.1371/journal.pone.0192633
call_split See protocol

[…] ity (Table B in ). Where no such sequences were available (for example, within dinoflagellates, and bodonids), combined transcriptome datasets were retrieved from a previously modified version of the MMETSP database that had previously been cleaned of potential contaminant sequences [, , ]. Other transcriptome datasets, which include, Trypanoplasma borreli, Trypanosoma theileri, Trypanosoma carass […]

library_books

A tale of two mixotrophic chrysophytes: Insights into the metabolisms of two Ochromonas species (Chrysophyceae) through a comparison of gene expression

2018
PLoS One
PMCID: 5811012
PMID: 29438384
DOI: 10.1371/journal.pone.0192439

[…] ies supplemented with additional chrysophytes and synurophytes was constructed using 18S rRNA gene sequences retrieved from GenBank or the Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP) database. A segment of 1,677 positions on the 18S rRNA gene was selected through a combination of Gblocks [] and manual editing to use for tree building using MUSCLE []. Approximate maximum li […]

library_books

A global ocean atlas of eukaryotic genes

2018
Nat Commun
PMCID: 5785536
PMID: 29371626
DOI: 10.1038/s41467-017-02342-1

[…] p://www.genoscope.cns.fr/tara/. Unigenes without Pfam domains are excluded from analyses presented in Figs. , and Supplementary Figs. , , , . The Pfam domain PF01036 was searched in unigenes and the MMETSP collection using hmmscan (from HMMer 3.1b2). NCBI sequences carrying the Pfam motif were retrieved through the PFAM portal (http://pfam.xfam.org/, May 2017). All-vs.-all BLAST comparisons were […]

Citations

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MMETSP institution(s)
Department of Botany, University of British Columbia, Vancouver, BC, Canada; Canadian Institute for Advanced Research, Integrated Microbial Biodiversity program, Canada; [etc]
MMETSP funding source(s)
This project was funded by the Gordon and Betty Moore Foundation (GBMF; Grants GBMF2637 and GBMF3111) to the National Center for Genome Resources (NCGR) and the National Center for Marine Algae and Microbiota (NCMA).

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