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Protocols

NEMBASE specifications

Information


Unique identifier OMICS_03133
Name NEMBASE
Restrictions to use None
Maintained Yes

Taxon


  • Invertebrates
    • Caenorhabditis elegans

Maintainer


  • person_outline John Parkinson

Publication for NEMBASE

NEMBASE citations

 (25)
library_books

Comparative analysis of pre and post parasitic transcriptomes and mining pioneer effectors of Heterodera avenae

2017
PMCID: 5309974
PMID: 28289537
DOI: 10.1186/s13578-017-0138-6

[…] ) strategy was used in the nematode ESTs comparisons. All the nematoda ESTs, consisting of 1,331,401 ESTs sequences from 45 genuses and 75 species clustered into three life styles, were from NCBI and Nembase 4 [] databases (Additional file : Table S2). […]

call_split

Strong LAMP: A LAMP Assay for Strongyloides spp. Detection in Stool and Urine Samples. Towards the Diagnosis of Human Strongyloidiasis Starting from a Rodent Model

2016
PLoS Negl Trop Dis
PMCID: 4945066
PMID: 27415764
DOI: 10.1371/journal.pntd.0004836
call_split See protocol

[…] sequences reported for possible human pathogens were detected. The 329 bp sequence selected was also tested in silico for similarity in the currently available genome databases for S. stercoralis at NemBase4 (www.nematodes.org) and a 94% identity with a partial sequence in contig SSC06134_1 annotated for the parasite was obtained. Forward and backward outer primers (F3 and B3) and forward and bac […]

library_books

Polymorphism in ion channel genes of Dirofilaria immitis: Relevant knowledge for future anthelmintic drug design

2016
PMCID: 5196487
PMID: 27682347
DOI: 10.1016/j.ijpddr.2016.06.003

[…] f all nematodes were extracted from available databases such as NCBI (http://www.ncbi.nlm.nih.gov/), Wormbase (http://www.wormbase.org/#01-23-6), Broad Institute (https://www.broadinstitute.org/) and NEMBASE4 (http://www.nematodes.org/nembase4/). These sequences were then blasted (BLASTN 2.2.25) () in the nucleotide blast server v2.2 (http://nematodes.org/genomes/dirofilaria_immitis/) to locate ea […]

library_books

A preliminary proteomic characterisation of extracellular vesicles released by the ovine parasitic nematode, Teladorsagia circumcincta

2016
PMCID: 4867787
PMID: 27084478
DOI: 10.1016/j.vetpar.2016.03.008

[…] ng the FDR at a stringency of 1% did not result in the exclusion of any proteins that were confidently identified in the original database search and validation. The results in ProteinScape™ from the Nembase4 search included the sequence ID of each protein. Subsequently, each protein sequence from Nembase4 was subjected to a manual Blast procedure (tblastn) against the full NCBInr database to find […]

library_books

Horizontal gene transfer of acetyltransferases, invertases and chorismate mutases from different bacteria to diverse recipients

2016
BMC Evol Biol
PMCID: 4828791
PMID: 27068610
DOI: 10.1186/s12862-016-0651-y

[…] igrada (water bears) is another basal Ecdysozoa phylum like Nematoda. Also, we performed tblastn and blastp searches against all nucleotide and protein databases available at Nematodes.org, including NEMBASE4 [], using an E-value threshold of 1E-04 (the online server did not allow 0.001). Furthermore, we performed blastn or tblastn searches against the raw sequence data obtained from the following […]

library_books

A transcriptomic insight into the infective juvenile stage of the insect parasitic nematode, Heterorhabditis indica

2016
BMC Genomics
PMCID: 4774024
PMID: 26931371
DOI: 10.1186/s12864-016-2510-z

[…] scripts (>300 bp) was done using blastp [], homology search against Uniprot [], the National Center for Biotechnology Information (NCBI)-NR Protein database [] and NEMABASE4 (http://www.nematodes.org/nembase4/). In addition, blastx was performed to identify homologues at ≥30 % query coverage and ≥50 % sequence identity and e-value 1e–5 in other databases including RefSeq (PRK), SWISSPROT [], Europ […]

Citations

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NEMBASE institution(s)
Institute of Cell, Animal and Population Biology, Ashworth Laboratories, King's Buildings, University of Edinburgh, Edinburgh, UK

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