NNPP pipeline

NNPP specifications

Information


Unique identifier OMICS_17686
Name NNPP
Alternative name Neural Network Promoter Prediction
Interface Web user interface
Restrictions to use None
Input data A protein sequence.
Input format FASTA
Computer skills Basic
Stability Stable
Maintained Yes

Taxon


  • Invertebrates
    • Drosophila melanogaster

Publication for Neural Network Promoter Prediction

NNPP IN pipelines

 (6)
2016
PMCID: 4789750
PMID: 26971572
DOI: 10.1038/srep22636

[…] respectively3132. the putative functions of the orfs were analyzed by blastp searches at the national center for biotechnology information (ncbi). putative promoter regions were predicted using the neural network promoter prediction tool of the berkeley drosophila genome project (minimum promoter score: 0.9)33. rho-independent transcription terminators were identified using finding terminators […]

2016
PMCID: 4942445
PMID: 27462508
DOI: 10.1186/s40064-016-2693-4

[…] calculator program (innovagen, http://www.pepcalc.com). nucleotide sequences alignment was performed using the genetyx-mac software (genetyx®, japan). promoter prediction was performed using the neural network promoter prediction software (http://www.fruitfly.org/seq_tools/promoter.html). protein sequences alignment was performed using the bioedit sequence alignment editor program v.7.0.0 […]

2013
PMCID: 3757033
PMID: 24009504
DOI: 10.1371/journal.ppat.1003571

[…] of smpomuc genes, cloning and sequencing”., the 5′utr and orf were previously characterised using 5′race-pcr experiments [56]. the core promoter including a tata box and the tss was predicted using neural network promoter prediction tool (http://www.fruitfly.org/seq_tools/promoter.html) [57]. we identified repetitive elements in the promoter region sequences using the censor software [58]. […]

2008
PMCID: 2440308
PMID: 18584054
DOI: 10.1371/journal.pone.0002375

[…] databases using blastp, followed by manual curation. comparative genome analysis was performed by using the artemis comparison tool (act; www.sanger.ac.uk_software). promoter region was analyzed by neural network promoter prediction (http://www.fruitfly.org/seq_tools/ promoter.html). the atlas of genome is drawn using genomeviz1.1 [67]., m. tuberculosis h37rv and h37ra were grown in middlebrook […]

2008
PMCID: 2459278
PMID: 18474600
DOI: 10.1074/jbc.M801223200

[…] was analyzed for the presence of repeat regions and transposable elements, using repeat masker version open-3.1.5. confirmation of pol ii promoter was conducted with promoter scan ii and novel neural network promoter prediction. identification of cpg islands was performed using cpgprod (cpg island promoter detection) software. in silico analysis for transcription factor-binding sites […]

NNPP institution(s)
Berkeley Drosophila Genome Project, Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
NNPP funding source(s)
This work was supported by NIH grant HG00750.

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