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Citations per year

Number of citations per year for the bioinformatics software tool Metazome
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Protocols

Metazome specifications

Information


Unique identifier OMICS_21286
Name Metazome
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Version 3.2
Maintained Yes

Taxon


  • Invertebrates
    • Bombyx mori
    • Caenorhabditis elegans
    • Drosophila melanogaster
  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus
    • Rattus norvegicus
  • Vertebrates
    • Danio rerio
    • Gallus gallus
    • Xenopus tropicalis

Maintainer


  • person_outline Metazome Team

Additional information


https://metazome.jgi.doe.gov/pz/QuickStart.html

Metazome citations

 (21)
call_split

An evaluation of the evolution of the gene structure of dystroglycan

2017
BMC Res Notes
PMCID: 5216574
PMID: 28057052
DOI: 10.1186/s13104-016-2322-x
call_split See protocol

[…] All the gene sequences investigated were retrieved either from the Ensembl database [] or from the Metazome v3.0 database from the University of California (http://www.metazome.net). Searches were completed as of the end of January 2016. Searches with protein sequences were performed by BLASTP at N […]

library_books

The evolution of genes encoding for green fluorescent proteins: insights from cephalochordates (amphioxus)

2016
Sci Rep
PMCID: 4911609
PMID: 27311567
DOI: 10.1038/srep28350

[…] a), the sea snail limpet Lottia gigantea (Mollusca) and the acorn worm Saccoglossus kowalevskii (Hemichordata) from EnsemblMetazoa (http://metazoa.ensembl.org) (for S. purpuratus and L. gigantea) and Metazome v3.0 (www.metazome.net) (for S. kowalevskii). GFP-encoding gene was screened by hmmsearch (option: -E 1e-4) for these proteomes. […]

library_books

Tentacle Transcriptome and Venom Proteome of the Pacific Sea Nettle, Chrysaora fuscescens (Cnidaria: Scyphozoa)

2016
Toxins
PMCID: 4848628
PMID: 27058558
DOI: 10.3390/toxins8040102

[…] 1 October, 2013); (b) Cnidarian protein sequences from the GenBank non-redundant (nr) protein database; (c) the complete genomes and transcriptomic data sets of H. vulgaris and N. vectensis from the Metazome project []; and (d) the UniProt animal toxin and venom database [,]. The transcriptome was functionally annotated using InterProScan (version 5) [] and Blast2GO (version 2.5) []. Proteins wer […]

library_books

Reassessing ecdysteroidogenic cells from the cell membrane receptors’ perspective

2016
Sci Rep
PMCID: 4742824
PMID: 26847502
DOI: 10.1038/srep20229

[…] data from PGs of day 4, 5th instar B. mori larva in an attempt to identify additional proteins not identified by our method. Comparisons with that dataset were generated using the BLASTP algorithm on Metazome v3.0 (http://www.metazome.net/search.php?show=blast&method=Org_Bmori) and are reported on . […]

library_books

Calcareous sponge genomes reveal complex evolution of α carbonic anhydrases and two key biomineralization enzymes

2014
BMC Evol Biol
PMCID: 4265532
PMID: 25421146
DOI: 10.1186/s12862-014-0230-z

[…] axa were obtained from GenBank [] or identified by BLAST searches against data from sequenced invertebrate genomes [,-] and transcriptomes [] from data of publicly available sources: Compagen [,] and Metazome v3.0 [] (Additional file ). In Hydra, we excluded some proteins, which had additional domains and only partial CA-domains. Sequences were aligned with MAFFT version 7 [] and sites for phyloge […]

library_books

The Early Expansion and Evolutionary Dynamics of POU Class Genes

2014
Mol Biol Evol
PMCID: 4245813
PMID: 25261405
DOI: 10.1093/molbev/msu243

[…] RIKLGYTQTNVGEALAAVHGSEFSQTTICRFENLQLSFKNACKLKAILSKWL. Sequences from Hydra, Nematostella, Lottia, Caenorhabditis, Tribolium, Drosophila, Strongylocentrotus, Xenopus, Mus, and Homo were collected from Metazome (http://www.metazome.net/, last accessed August 24, 2014) using BLASTP against the predicted proteomes. For A. queenslandica, we used TBLASTN against the Spongezome Metazome database (http:// […]


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