PromoSer protocols

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PromoSer specifications

Information


Unique identifier OMICS_09569
Name PromoSer
Interface Web user interface
Restrictions to use None
Input data List of GenBank accessions or FASTA sequences
Output data PromoSer reports the number of accessions for which a promoter could be identified.
Computer skills Basic
Stability Stable
Maintained No

Taxon


  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus
    • Rattus norvegicus

Maintainer


This tool is not available anymore.

Publications for PromoSer

PromoSer in pipelines

 (4)
2009
PMCID: 2655687
PMID: 19139068
DOI: 10.1093/nar/gkn1085

[…] positions ±1000 nt were retrieved from the genome browser database. nucleotide sequences of promoters (2000 nt upstream of tss) for randomly selected gene accession numbers were retrieved from the promoser database (http://cagt.bu.edu/page/promoser_submit) (). the content of repetitive sequences was analyzed using the repeatmasker server (a.f.a. smit, r. hubley and p. green; […]

2007
PMCID: 1802077
PMID: 17286855
DOI: 10.1186/1471-2164-8-42

[…] as well as non-retinal ests to obtain the most complete information about the different alternative start sites already mapped. additionally, the information about putative tss was assessed using promoser [], eukaryotic promoter database current release 87 [], and database of transcriptional start sites dbtss []. first exon boundaries were determined by aligning the predicted sequence […]

2007
PMCID: 2258200
PMID: 18021424
DOI: 10.1186/gb-2007-8-11-r244

[…] graph metric in the randomized ensemble., the fasta sequences of the promoters, including 1,000 bp upstream and 50 bp downstream of each transcription start site, were extracted from the promoser database []. the predicted binding sites of genes were obtained according to the categories of tfs from groups a to f with the aid of the existing nomenclature and phylogenetic analysis. […]

2005
PMCID: 1173081
PMID: 15904489
DOI: 10.1186/1471-2105-6-121

[…] or to genes including in their sequence record words referring to vision, eye or retina., retrieval of promoter sequences corresponding to 1 kb upstream the predicted tss of genes was done by promoser [,]. tss prediction options were set in order to retrieve for each gene 1 kb upstream the most 5' tss, with the same criteria used for retrieval of retinal gene promoters. in addition, […]


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PromoSer in publications

 (13)
PMCID: 5539417
PMID: 28791126
DOI: 10.1038/cti.2017.32

[…] by 32p transfer to sphingosine in vitro, as described previously., promoter sequences 1000 bp upstream, and 50 bp downstream from the transcription start site, were obtained for each gene using promoser. potential transcription factor-binding sites were identified using matinspector (genomatix suite, muchen, germany)., all experiments were performed at a minimum of duplicate samples […]

PMCID: 4134504
PMID: 25010866
DOI: 10.1038/bjc.2014.372

[…] putative promoter regions of amot-p80 and mir-146a were identified using in silico analysis using http://rulai.cshl.edu/cgi-bin/cshlmpd2/promextract.pl?species=human (), http://biowulf.bu.edu/zlab/promoser/ () and http://www.genomatix.de/solutions/genomatix-software-suite.html (). to clone the promoter sequences into pgl3-basic luciferase reporter vector, sequences of xhoi and hindiii […]

PMCID: 2951341
PMID: 20949099
DOI: 10.1371/journal.pone.0013150

[…] regions (1000 bp upstream of the transcriptional start site) of 20 of the 23 genes clustered with wap were obtained using ezretrieve. (http://siriusb/umdnj.edu:18080/ezretrieve/index.jsp) and promoser (http://biowulf.bu.edu/zlab/promoser). the upstream sequences for the genes acbd7, ighg and gm566 were not identified by these programs. putative promoter sequences were searched using […]

PMCID: 2713694
PMID: 19536094
DOI: 10.1038/sj.bjc.6605111

[…] is, the genes that were correlated in at least three out of 100 microarray data sets (). we also used the 85 mitoribosomal genes for sequence analysis. gene promoter sequences were extracted by the promoser web server from −1000 to +1000 nucleotides starting from the transcription start site (tss) (). promoser retrieved 69 out of 331 sequences of the dap3 coexpressed genes, and 71 out of 85 […]

PMCID: 2655687
PMID: 19139068
DOI: 10.1093/nar/gkn1085

[…] positions ±1000 nt were retrieved from the genome browser database. nucleotide sequences of promoters (2000 nt upstream of tss) for randomly selected gene accession numbers were retrieved from the promoser database (http://cagt.bu.edu/page/promoser_submit) (). the content of repetitive sequences was analyzed using the repeatmasker server (a.f.a. smit, r. hubley and p. green; […]


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PromoSer institution(s)
Bioinformatics Program, Boston University, Boston, MA, USA; Biomedical Engineering Department, Boston University, Boston, MA, USA

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