promoterwise protocols

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promoterwise specifications

Information


Unique identifier OMICS_17613
Name promoterwise
Interface Web user interface
Restrictions to use None
Input data Two DNA sequences.
Input format GCG, FASTA, EMBL, GenBank
Output format PSEUDOBLAST,XML,TAB
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Rodrigo Lopez <>

Additional information


https://www.ebi.ac.uk/Tools/psa/promoterwise/help/

promoterwise in pipeline

2005
PMCID: 1273639
PMID: 16086854
DOI: 10.1186/gb-2005-6-8-r72

[…] genes is in [], all known promoters in cshlmpd can be downloaded from []., we thank lisa stubbs for providing experimental testing results before publication. we thank ewan birney for providing promoterwise software, lincoln stein for providing gbrowse. this work is supported by nih grants hg01696, gm60513, ca88351, and hg002600., *number of genes in non-overlapping gene types. †number […]


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promoterwise in publications

 (8)
PMCID: 5635497
PMID: 29046813
DOI: 10.1186/s40575-017-0050-8

[…] gstp1 promoter and transcript sequences was performed using clustal omega [] in order to determine the degree to which the sequences are conserved. pairwise sequence alignment was computed by promoterwise [], which allows for inversions and translocations that are common in promoters. the aligning of transcription factors to the canine gstp1 promoter sequence was performed by using […]

PMCID: 4884571
PMID: 27071403
DOI: 10.1007/s11103-016-0473-8

[…] in saffron (ahrazem et al. ). in order to identify other putative common regulatory elements in both promoter sequences, we compare the csccd2b promoter with the promoter of cslycb2a using the promoterwise program (mcwilliam et al. ). seven common sequences were identified (table ) that does not correspond to any of the previously identified cis-regulatory elements.table 4, the in silico […]

PMCID: 4702614
PMID: 26475115
DOI: 10.1128/AEM.01968-15

[…] context of slap genes was examined using the chromosomal graphical interface in geneious 8.0.5. in silico promoter elements were identified in the upstream intergenic regions of slap genes using promoterwise (http://www.ebi.ac.uk/tools/psa/promoterwise/). to identify conserved promoter elements between the various slap genes, genome-wide sequence motifs of the putative −10 and −35 regions […]

PMCID: 2654921
PMID: 19305507
DOI: 10.1371/journal.pone.0004961

[…] the european bioinformatics institute's clustalw tool () for phylogram analysis after multiple sequence alignment of the respective promoters. to confirm homology quantitatively, we used embl-ebi's promoterwise comparison tool which found significant pair-wise areas of promoter homology in gpr17, grin1, and tktl1. as expected from earlier studies, the mage-a family clustered together, […]

PMCID: 1988851
PMID: 17892326
DOI: 10.1371/journal.pgen.0030159

[…] [,]. since our aim is to identify conserved target genes, we also searched for motifs within the ath5 regulatory region that are conserved throughout vertebrates. in a comparative approach using promoterwise (http://www.ebi.ac.uk/~birney/wise2/) we identified two evolutionarily conserved (from teleosts to mammals) extended e-box motifs (ccacctg) within 2 kb of upstream sequences […]


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