Motif Locator statistics

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Motif Locator specifications

Information


Unique identifier OMICS_15391
Name Motif Locator
Interface Web user interface
Restrictions to use None
Output data A set of coordinates in the analyzed DNA sequence.
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Jan Mrazek <>

Motif Locator in publications

 (6)
PMCID: 3940949
PMID: 24595272
DOI: 10.1371/journal.pone.0090940

[…] in e. coli k12. the binding potential of each nap in a chromosomal region was measured by the number of its predicted binding sites in that region. the binding sites were predicted using the motif locator program (http://www.cmbl.uga.edu/software/motloc.html), which applies the standard position-specific score matrix (pssm) model. a collection of known binding sites used to build […]

PMCID: 3844500
PMID: 24007446
DOI: 10.1186/1471-2164-14-602

[…] was based on the consensus sequence for σ54-dependent promoters defined by barrios et al. [] and comparison analysis of the known salmonella σ54-dependent promoters. this pssm was applied with the motif locator program [] to the enriched orf sequence and 1000 bp of flanking sequence on both sides of the orf to identify potential σ54 dna binding sites. the size range of dna fragments […]

PMCID: 3287487
PMID: 22784578
DOI: 10.1186/1752-0509-5-S2-S7

[…] genes, while a low score indicates that the motif occurs many times in a part of promoters of down-regulated genes. the number of each motif presence in a promoter was then counted with using weeder-motif locator program, with options as minimum match percentage; 90 percent, search the motif in both strands; check, maximum number of substitutions; substitutions: 1 ; n=6,8,: 2 ; n=10,12, : 3 ; […]

PMCID: 3121120
PMID: 21689479
DOI: 10.1186/1752-0509-5-S1-S4

[…] the regulatory network being mapped are the query sequences. the output of blast is a set of similar tgs that are then the input for the next step of locating the binding sites. the binding site motif locator searches for the tfbs motifs of the source genome tf in the similar tg sequences found in the target genome. finally, the genes that are similar (found using blast) and have the right […]

PMCID: 2817457
PMID: 19933264
DOI: 10.1093/nar/gkp1028

[…] conserved regions. however, adenovirus is non-replicative in rodents, so sequence conservation should not be taken into consideration to define putative targets of mivarnas. thus, we decided to use motif locator, which searches for a given sequence in all the genes included in a database. motif locator was used to identify seed complementary target sequences in the 3′utr of all the genes […]


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